BIOVIA Materials Studio
Materials Studio Training Registration
Hello everyone, I’m interested in enrolling in Materials Studio training aligned with the courses listed in your course catalog. Could you please share the registration process, upcoming schedules, and pricing/licensing details?
CASTEP MEP error
Dear all, Hope you all have a great day. I tried CASTEP MEP calculation, but it always fails with the same error message. "Cold fusion diagnosed - STOP. Energy and limit: -1517247.537 -1000000.000" The details are below: System (bulk hopping path) Material: Bulk ceria (CeO₂), cubic fluorite–type supercell, a = b = c = 10.9956 Å, α = β = γ = 90° (3D PBC, no vacuum). Composition: 94 atoms total — Ce 32, O 62 (i.e., O-deficient vs. the 2×2×2 fluorite cell; two O vacancies present).
how to represent the A-site mixed occupancy in a Crystal Structure
Hello dear all. Please, how do I represent the A-site mixed occupancy of 1.1 Nitrogen, 1 Carbon and 6 Hydrogen Atoms in the I4cm Tetragonal MA₀.₉₅GA₀.₀₅PbI₃ Crystal Structure knowing that no fractional atoms exist in a single unit cell? In fact I want to see the effect of GA composition when mixed with MA cation in MAPbI3... So I will need to do that process a couple of time when changing the GA proportion into the A-site cation of perovskite. Your help will be highly appreciated
Converting .xtd/.car Files to LAMMPS .data
I’m currently working on a crosslinked polymer system that I’ve built and equilibrated in Materials Studio. I’m trying to convert my model (in .xtd / .car format) to a LAMMPS .data file for simulation, but I don’t have access to the Pipeline Pilot Run LAMMPS MD protocol. Would anyone with a Pipeline Pilot license and access to this protocol be willing to help me convert a few files? I can share the .xtd and .car files directly, and would greatly appreciate the help. I’ve tried using msi2lmp with
Forcefield for Naphthalene
I want to simulate pure Naphthalene in Materials Studio at 20 °C and 1 atm. In the NPT ensemble, the density tends towards 0. The forcefield used for it was COPMASS III. What should I do? Additionally, I also checked other force fields like COMPASS and Universal, but it didn't work.
Interaction energy using DFT
Dear MS Community, I came across a research paper,https://pubs.acs.org/doi/10.1021/acs.cgd.7b00163. In this paper, the authors have calculated the binding interaction energy using DFT in Gaussian 09 software. For geometry optimization, they used the B97-D3 Grimme function with the Gaussian-type 6-31(d,p) basis set. And for energy calculations, they used the double hybrid B2PLYP-D3 function with def2-QZVPP as the basis set. They calculated the Interaction Energy (IE) for API with different
Need to calculate mechanical loss(tan delta)
How do I use Materials Studio to calculate mechanical losses for cross-linked polymers, is there a script to implement it?
Xlink.pl The open ring is not working.
Hello. I'm trying to do a crosslinking simulation for an epoxy polymer. If you check all options again, the crosslinked model will not open the epoxide ring. I'd appreciate it if you could check it out.
CEF update
I am getting a message that an update is required for the CEF when I launch 3D Annotation Insight desktop shortcut. The problem is that I can't figure out how to update that. Any help would be greatly appreciated.
Effect of Surface Calculation on Atoms Positioned on Lattice
Dear all, I hope this message finds you well. I would like to share a recent issue regarding the (100) surface calculation of a vanadium nitride structure using the DMol3 module. The default cutting plane for the surface had u and v vectors set as u (0, 0.5, -0.5) / v (0, 0.5, 0.5). However, in order to preserve the original shape modelled previously, I modified the vectors to u (0, 1, 0) / v (0, 0, 1). I will attach images and the xsd file to illustrate the difference between the two surface
Molecular Selection
Hello Everyone, I just wanted to know, is there any way to select all same molecules within amorphous cell? I need to perform concentration analysis. I have tried selection through forcefield type but some other atoms get selected during forcefield type selection. Thanking in Advance
Material studio download
How can I get the material studio, download link. I have the licence in my lab
installation quarry
Can I install Material Studio in my Windows system?
Free volume calculation script
Hello, friends of the community. I need a script about xtd free volume calculation + analysis function. Thank you very much.
Calculate the dielectric constant script using the dipole moment
Hello users in the community, I am using a script that uses the dipole moment to calculate the dielectric constant of polypropylene, why is it calculated to be about 1.2, but the experimental value is 2.2-2.3? And the dielectric constant calculated by this script is 24.4, which is far from the experimental value of 36-38, anyone can answer my question thank you.
Radius of Gyration Issue
Hi everyone, I'm performing Dissipative Particle Dynamics (DPD) simulations using the MesoDyn module in BIOVIA Materials Studio 2022 (version 22.1.1.11). My system consists of PNIPAM polymer chains grafted onto a silica substrate, with water as the solvent. I aim to study the temperature-dependent conformational changes of the polymer by calculating the radius of gyration of PNIPAM chains from trajectories obtained at different temperatures (278 K, 298 K, and 308 K). However, when I attempt to
Encapsulation Studies
Hello, How do I perform encapsulation studies of OPV in Materials Studio? Thanks.
DMol3 Optimization Problem: How to solve?
Dear Community members, I am optimizing an Organic simple-structure in 3D atomistic file. During Optimization calculation gives the following error. Can anybody suggest how to solve it? Probably it is a very silly mistake, however, I am unable to resolve it after several trials. The message was: Publications of specific relevance to this calculation: Density functional: PBE functional: Perdew Burke Ernzerhof: Phys. Rev. Lett. 77, 3865 (1996) Spin unrestricted calculation The Generation and
Biovia Draw 2025 Academic Edition is not detected by Biovia Desktop Connector 2025
Hello, does anyone have the same issue ? On a fresh install of windows 11 pro 24h2 64-bits, fully up-to-date, i've installed the new version of Biovia Draw Academic Edition (25.1.0.2318) and the Desktop Connector in version 25.1.0.312. Biovia desktop connector does detect, Marvin, office and ChemDraw, but it does'nt detect at all Biovia Draw (either in 64-bits and in 32-bits, i tried to install the 32-bits version in-place of the 64-bits as it was not detected, but does the same) It does
Resolve an error while running calculation on MS
i cannot run the calculations on material studio using any module.i found an error "Can't create a job for the server:Forcite. This computer was unable tocommunicate with the computer providing the server". please help me to resolve this.
Construction of kerogen pore model in MS software ; the process of gas-water displacement in pores
Hello experts, everyone. I am now ready to study the mechanism of gas-water competitive adsorption in shale / coal, and encounter two obstacles in the process of research. First, it is necessary to simulate the gas-water distribution characteristics of different pore models in kerogen cells, such as slit-type, circular, square, and triangular pores ( Fig.1 ). How to construct the pore morphology in MS software ? Secondly, for the constructed fracture-type pores, we want to realize the dynamic
Plotting partial density of states dxy, dxz, dyz, dx2−y2, dz2
Hi, I would like to plot the partial density of states in terms of dxy, dxz, dyz, dx2−y2, dz2. Currently, in CASTEP, we can plot PDOS as s, p, d and f orbitals versus energy But, I would like to plot only d-orbital, but in the form of as t2g and eg orbitals (dxy, dxz, dyz, dx2−y2, dz2). Any manual calculations needs to be done using the PDOS we get? If yes, could any one help me please with this. Thank you
Young's modulus
When using the forcite module to calculate Young's modulus, why do negative values appear? Can the forcite module be used to calculate the Young's modulus of polymers, or is it only applicable for calculating the Young's modulus of crystals?
MS独立控温脚本如何写
研究初始温度的液滴在一个环境条件下的蒸发
How to set salt in solid-liquid module
we are trying to find eutectic points for low eutectic solvents by COSMOtherm 2020. The examples in the guidebook have been reproduced perfectly. But there is no mention of how to set up a salt compound like choline chloride. Choline chloride, the primary solvent, is present in the TZVPD database as the cations choline_cation and CL_anion. I've looked at all the community articles about ‘choline chloride’, “DES” and ‘deep eutectic solvent’, and so on. etc. I didn't find any explanation. I've
Materials Studio on Supercomputer
Dear MS community, My lab purchased Materials Studio last year in March 2024, and it was successfully installed on our personal workstation. I wanted to know if we can utilize our institute's Supercomputer to run the software without actually installing on it. We just want to use the advanced computing power of the Supercomputer to run our simulations faster. Please let me know the procedure. Regards.
CASTEP Band Structure
Dear all, I would like to understand how CASTEP in Materials Studio converts the raw band structure data from the output file foo.bands into the format used for plotting the band structure, which can be exported as a CSV file. I am not looking for the script used in this conversion or the plotting itself; rather, I want to understand how to manually perform this conversion. Specifically, I am interested in the step-by-step calculations involved, so that I can verify the first few data points
Purchase materials studio
I m interested to purchase BIOVIA materials studio
Webinar: Accelerating Scientific Research with BIOVIA Solutions for Education
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Solvation Free Energy
Hi MS Community, This is regarding calculating Solvation Free Energy (SFE) using Forcite module. So, basically I wanted to calculate SFE of Paracetamol (PCM) in Acetone (and in various other solvents and wanted to corelate it with the experimental values at 303.15K). I made two attempts with Acetone as solvent. Attempt-1: PCM molecules- 1 Acetone- 100 SFE turned out to be -94.295 kcal/mol which is highly unlikely. Now if you apply the formula, Solubility= exp( -SFE / RT) (provided by @TM in one
Learning MS Script
Hello community, I hope my message finds you well. I am a user of Materials Studio (MS) software, which I use mainly for calculations of adsorption, interactions and dispersion forces. However, I have noticed that the values obtained are abnormally high compared with those reported in similar studies, even though they were carried out using comparable parameters. I would therefore like to test the use of scripts in MS to better understand and identify the source of the problem.
CASTEP job automation (Perl script)
Dear all, I would like to automate running a series of jobs each with a different cutoff energy. I read the scripting manual but couldn't figure it out how to correctly do this. I did generate and save the input files, and also created a Perl script document inside my project directory . How to write a script to run a series of jobs with different cutoff energies, say for example from 500eV to 600eV in steps of 25eV? I am using Materials Studio 2024 (Default installation) on Windows 11. Any
BIOVIA announces the release of BIOVIA Materials Studio 2025 SP1
BIOVIA Materials Studio 2025 SP1 was released in June 2025 and is available for download at https://software.3ds.com under BIOVIA products: Product line: Lab, Scientific and Content Solutions Release: BIOVIA 2025 Level: BIOVIA 2025 Refresh2 Fixes for this level: N/A The following Technical Note informs you about BIOVIA Materials Studio 2025 SP1 including the release's supported operating systems, enhancements and fixed defects. How to contact BIOVIA Support If you have any questions,
How to revise the script of Eint for XTD by Forcite for A, B, and C, three systems?
I'd like to calculate the Eint for corrosion inhibitors on Fe surface and already got the script of Eint for XTD by forcite from the official website, but it's only used for two systems. Here I need three systems to do it, I think, maybe A, B, and C. It means I need to define another system. It should be simple, but I don't know how to do it. Is there anybody who could help me? Appreciate!!
Help about Polymer making In materila studio
Can anyone help me by providing an information about material studio if I provide two polymer layers where atoms remain randomly (pdb file) can you make a model attaching these two layers in one in material studio?
Issue with Forsterite Supercell Deformation During Geometry Optimization (Forcite + COMPASS III)
I'm currently attempting to run a geometry optimization for a 2×1×1 supercell of forsterite using Forcite with the COMPASS III forcefield. However, the structure consistently becomes deformed after optimization. I’ve tried assigning atomic charges both manually and automatically, but the outcome remains nearly the same in both cases. Any suggestions or insights would be greatly appreciated.
ForciteDynamics fails after crosslinking
Hello everyone, I recently downloaded the `xLink.pl` crosslinking script and the associated `User Menu Jan4_2017.xml` from this community. I used the `DGEBAx32_13BDx32.xsd` file provided in the `sampleinputs` folder, which is already constructed as an amorphous cell. Here is what I did step by step: 1. Imported the `.xsd` file into Materials Studio 2. Performed Geometry Optimization to stabilize the structure 3. Registered `xLink.pl` and the XML menu in my project (confirmed successful – see
Visualizing Molecular Distribution in Sorption Module
I am currently working on determining the diffusion coefficient of a gas through a clay mineral's nanopore. As a preliminary step, I ran a Sorption module simulation to identify the locations of gas molecules within the pore space. However, the results appear to display a density distribution rather than the spatial distribution of individual gas molecules. I would greatly appreciate your guidance on how to obtain or visualize the molecules in the nanopore instead of just the density output.
How to extract exchange-correlation potential (not energy) in CASTEP?
Hello there, I’m currently working on DFT calculations using CASTEP, and I was wondering if there is any way to extract the exchange-correlation potential from a CASTEP run. I’m aware that the exchange-correlation energy is printed in the .castep output file, but my interest is in obtaining the exchange-correlation potential itself — either as a numerical grid or any form that could be visualized or post-processed. Is there a way to extract directly or indirectly? Any guidance or
An input file can't operate correctly.
I want to acquire a file of the NVT or NVE system by molecular dynamics. But when the procedure ending, the output incorrect.I would appreciate if you can share what you advice.
HBD and HBA form eutectic solvent
How to determine through COSMO-RS at what molar ratio between HBD and HBA a low eutectic solvent can be formed, and what is the corresponding temperature?
How to analyze and view the data on dielectric constant and dielectric loss in Foricte regarding frequency
Hello, everyone, Perhaps this inquiry is not about software usage, but I still want to try asking about it Firstly, when conducting molecular dynamics on a polymer model with 7,000 atoms, an electrostatic field was added. Due to the insufficiency of computing power, only a 5ns simulation was conducted Subsequently, extrapolation was carried out through the double-exponential function script. For frequency-related dielectric spectra, how should I analyze the data The horizontal coordinate
Help Needed!! Sending computation jobs on Material Studios to a High Performance Computing server (computer cluster)
Hello, I have been struggling to connect my MS software job control to a computer cluster to run heavy calculations and save on computational time. So far my problem has been connecting to the license server that is running on my MS computer. I cannot figure out if this is a firewall issue on the computer or on the HPC. It is probably beneficial to note that the MS computer can be pinged from the HPC, indicating that they can interact with each other. I am unsure how to proceed/troubleshoot
Biovia and Accessibility
Hello there, My apologies if this is not the proper place for this, but my workplace is looking into using the Biovia Draws product and I am needing to see if there is any accessibility information on it, especially a VPAT(Voluntary Product Accessibility Template) of it that I can access and see whether or not the software meets standards. Is anyone aware of accessibility documentation for Biovia?
The abscissa of the MS2024 dipole autocorrelation function when calculating the Permittivity Loss
Hello everyone! How can I convert the horizontal coordinate? Could anyone explain it
A further question for: Need Help: Building Quaternary Ammonium Salts (Choline Chloride) in TmoleX
Dear all, I am currently working on obtaining the sigma-profile and sigma-potential for quaternary ammonium salts, such as choline chloride. So far, I have loaded the cation (choline) and the anion (Cl⁻) from the database. Here are further questions: 1、Could you please advise on the next steps required to generate the sigma-profile and sigma-potential plots for choline chloride? 2. Additionally, I would like to model the system as an ion pair (commonly referred to as the AB model), rather than
how to solve "Uncovergenced issues"
Dear all, this job is Uncovergenced, how can I fix it? Can I just click on continue?
Question about calculating ionic conductivity using Green-Kubo relation in Forcite
Hi everyone, I would like to ask a question regarding the calculation of ionic conductivity in electrolytes. As shown in the attached paper (J. Phys. Chem. Lett. 2023, 14, 7718–7731; see the link below), there are two different approaches to calculate ionic conductivity: the Nernst–Einstein equation and the Green–Kubo relation. The conductivity from the Nernst–Einstein equation is relatively straightforward to obtain using the MSD curve to extract the diffusion coefficient. (1. Define the
TG script issue
Good afternoon everyone, I have encountered an issue with the Glass Transition Temperature (TG) script. Whenever I use COMPASS to calculate, it will report an error message indicating excessive energy and non physical steps. I don't know how to improve my script to avoid this problem. This compressed file contains my script and the object I want to run. I hope someone can help me. Thank you!
Need Help: Building Quaternary Ammonium Salts (Choline Chloride) in TmoleX
Dear all, I am currently working on modeling a deep eutectic solvent (DES) composed of choline chloride and lactic acid. Lactic acid is already available in the database, but choline chloride (CAS: 67-48-1), a quaternary ammonium salt, needs to be built manually in TmoleX. Unfortunately, I have no experience with modeling such compounds in TmoleX and I’m unsure how to start. Could anyone kindly provide step-by-step guidance or share any tips on how to properly construct and optimize a molecule
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(how) can you build a mesostructure template with the perl script?
I am writing a script in MaterialsStudio 2023 and I need to build a mesostructure with a certain cell length, which I calculate previously. The system should contain 2 slabs as filler. Does anyone has a suggestion for the perl code? scriptperlmesostructuretemplate
How to create 3D structure of amorphous SiO2?
Hi, I want to do md simulation of the amorphous SiO2 (with special physicochemical properties such as pore size, surface area and density) with a drug molecule. In first step, guide me how to obtain 3D structure of amorphous SiO2 by details. Best, LK
[CASTEP] Different Lattice Parameters with and without Imposing Symmetry
Dear all, When I geometry optimize my crystal structure in P1 symmetry, I obtain the following lattice parameters: a = 4.049465 Å b = 4.048257 Å c = 6.743723 Å α = 83.923486° β = 83.865180° γ = 62.441285° Cell volume = 97.247146 ų However, when I allow CASTEP to convert the structure to a higher-symmetry setting (using the prompt at the beginning of the geometry optimization), I get: a = 4.049562 Å b = 4.049562 Å c = 9.046694 Å α = 125.162434° β = 125.162434° γ = 62.433003° Cell volume
Seebeck coefficient using Materials Studio
Hi All, I would like to compute Seebeck coefficient for a functionally Graded Material using classical simulations. I have a layered structure consisting of 10,000 atoms. So, I would like to use either forcite or GULP. Could you please help me with the algorithm to follow and any scripting ideas for the computation. Thank you Regards Yamini
Forcite - No intermediate results available yet
I have been running NPT simulations in Forcite. This has been running successfully for >1us so far, however on the most recent Restart, the job "completes" instantly, and I get this message in Status.txt: "No intermediate results available yet!". There are no error messages in the log file, and no outputs (energies, density etc). Can anyone help?
perl script for nanoindentation
Hello everyone! May I ask if anyone has a script for nanoindentation testing? The main content of the script is to apply a radial pressure of the specified kcal/mol/Å along the direction of the red arrow in the figure and measure the indentation depth on the surface of the composite material under different radial pressures.It would be better if the test temperature could be set. Can anyone help me?
Help: After MD simulates NVE equilibrium and performs NPT heating, the system density becomes very small and cations and anions accumulate.
results of NPT Parameters of NPT
Material Studio scroll bar issue
Hi. I'm using Material Studio 2023 (23.1.0.3829). After loading a Perl script, the scroll bars get locked, so I can not navigate using the mouse wheel. When clicking on them and moving it, I just get the text of script selected. Any help is welcome. Thanks in advance, Hatuey
BIOVIA Materials Studio Academic License
Hello Everyone, I was wondering what was approximate price for Biovia Materials Studio for Students in academic laboratories? I am doing my PhD at San Diego State University and I work on amino acid adsorption on the surface of various morphology silica nanoparticles. I wanted to use CASTEP in BIOVIA materials studio for some of the simulations and NMR shift calculations, would it work for clusters/amino acids? Thanks in advance
TG script error
Hello everyone, I tried to run the Tg script by Stephen (Automate calculations for estimating glass transition temperature in polymers) to calculate the temperature of the polymer. I encountered the following error: Can't call method "Trajectory" on an undefined value at - e line 155. My Materials Studio version is 2023. Can anyone help me solve this problem? Thank you for any comments on this matter.
Metal oxides undergo geometric optimization and deformation in the COMPASS position
Seeking help from everyone, I have encountered a problem.The metal oxide in my model will deform after geometric optimization, and I am using the COMPASS position. I found that the reason may be due to the difference in charge caused by the unequal number of metal atoms and oxygen atoms in the nanocell, because the charge cannot be zero. However, even after manually balancing the charge, the nanocell still deforms during geometric optimization. I would like to consult with you for a solution.
DFT calculations for gas sensing mechanism with materials studio 2023
Hello community, I just joined in today. I am a materials science student without any knowledge in DFT but I want to learn it to my best. Actually, I want to apply it for gas sensing mechanism and performance analysis for different semiconductor materials. I have gone through some videos and AI scripts but somehow I am not satisfied and did not learn much. Can anyone please give me some directions on how to do these things in Materials Studio 2023? I will be forever grateful
MOF modelling and Simulation
Online training on modelling and simulations of MOFs is required for a beginner. Kindly assist.
Who has the experience about MD simulation for the Si2O effects on the Chain Compactness and Hydrated Network Behavior in PVA-HA Hydrogels?
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Marerilas stuido 2024 `s script : Multiple Trajectory DACF and Permittivity Loss Spectrum
Regarding the usage method of the script, it`s working principle, and possible output forms, is there any teacher who can explain it to me
BIOVIA Live 2025 Global | Customer Event
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How to properly export Materials Studio files for use in Discovery Studio (PDB issue with water molecules)
Hello everyone, I’m working with Materials Studio, and I generated an amorphous cell containing H₂O, a protein, a ligand, and several ions. I exported the structure as a PDB file, intending to use it in Discovery Studio. However, I noticed something strange — the water molecules don’t appear correctly when I open the exported PDB file in Discovery Studio. I’m wondering: Are there specific considerations or settings I should be aware of when exporting from Materials Studio to PDB format for use
Error in Amorphous cell construction
Dear All, I am getting an error while packing the species in the cell. I tried multiple times by changing various settings like Force Fields, loading steps etc. But nothing seems to work. The error says: Amorphous Cell calculation complete Status: Error Error description: Ran out of memory Previously, I have made cells much bigger than this. This is a very small cell as compared to my previous simulations, but still i am getting this error.
Molecule Displacement and Structural Adaptation in Simulation
Hello, I simulated a molecular system in a box and removed its central region to accommodate another molecule, slightly larger than its radius. After placing this molecular mass at the center of the box and optimizing the geometry, I observed that it shifted toward the bottom of the box. What could be the reason for this shift? Doesn’t this movement cause atomic overlaps or steric clashes?
Molecules coming out of the box
Why are molecules coming out of the box? Does this mean that the cell has not reached equilibrium? What should be done to solve it? (NPT - T = 683K)
Mesocite, micellar aggregation
Dear colleagues, I would like to inquire whether there are any existing scripts or other computational approaches to determine the number of clusters in Mesocite. For instance, after performing DPD simulations to observe micelle formation, I need to analyze the resulting aggregates—specifically, their quantity and aggregation numbers. Any guidance or references would be greatly appreciated.
Please help me
I am a graduate research student. Can you tell me how to buy and the price of the Dmol3 student license package for Materials Studio?
How can COSMOtherm X25 conduct High-throughput calculation ?
Dear BIOVIA Community, I am currently exploring how to perform high-throughput calculations using COSMOtherm X25. I understand that COSMOtherm can be operated through the command line to automate tasks, and I have already referred to the document Global Command and Comment Lines.pdf and a few example cases provided (mainly in BIOVIA_COSMO\therm\COSMOtherm2025\COSMOtherm\EXAMPLES). However, I find that the available materials are relatively limited for beginners. Specifically: Is there a more
Smeared Charges in MesoCite DPD Simulations
Dear colleagues, I am a PhD student currently working on modeling charged surfactant systems in MesoCite. The documentation ("Tasks in Mesocite") mentions the option to "use smeared charges," but I would appreciate some clarification on the implementation details. Should the charges be assigned to the beads directly in the Properties Explorer, or is it preferable to define them via the "Types/Interactions" section within the Forcefield Document? In the "Electrostatic Interaction" tab (Forcefield
Student Buying Materials Studio
Hello everyone, I can't find downloading link for materials studio. I have contacted for support for three days and I haven't got replies. I also want to get certification of materials studio. What should I do? Best wishes, Ruixian
PPPM
It is shown in the previous materials that the summation methods used to calculate the static dielectric parameters are Ewald and Group-based, and they have different calculation formulas respectively. However, GPU acceleration only supports PPPM. Then, whether PPPM supports the calculation of static dielectric parameters should be based on which formula?
Material studio Software license
Hi, everyone! Apologies if this question isn't very chemistry-related. The salesperson directed me here. I just wanted to ask how I can purchase/obtain the software and license, and if there are any student discounts available. I’ve browsed the website a few times but couldn’t find the information on how to obtain it, so I hope someone here can help.
Running a job in HPC
Hello everyone, I am trying to run a job in linux machine using DMol3 but i am getting the following error. Exclaimer: The parameter used for the water were tested and are correct. Everything is done through the main node and there is 1 computing node connected. Could this error be due to a configuration issue specific on the cluster?
[CASTEP] Different DOS k-point grid in result file than what was set in input
Hello, I'm running a CASTEP calculation using Materials Studio and encountered something confusing regarding the k-point settings. For both the SCF and DOS calculations, I explicitly set the k-point grid to 4×4×4. However, when I check the result file (specifically the .kptaux file), it appears that the SCF k-points are listed as 4×4×4, while the DOS k-points are shown as 6×6×6. I’ve attached screenshots showing the k-point settings used in the calculation as well as the relevant part of the
DPD Mesocite .off file
Greetings, I am using Material Studios to perform DPD simulations on mixtures with several components inside. I calculated the DPD parameters separately and then manually input them in Mesocite "Force-field manager" for cases where I do not have too many beads. However, I am now sutdying a case with severeal dozens of different beads and manually input all the possible bead pair parameters is just unfeasable. Is there any automated tool I could use to speed up the Mesocite force field file
Unique Bond Lengths and Angles
Dear all, How to use the "Unique Bond Lengths and Angles" script in Materials Studio? I have an optimized crystal structure (from CASTEP), say X.xsd. When I run this script it creates a folder in the project explorer with three files: X.xsd, CalcUniqueBondLengthAngles.pl, and CalcUniqueBondLengthAngles.pl.out I can not see any bond lengths and angles of my structure. Any help is much appreciated.
Amorphous Cell construction
Dear MS Community, I’m working with a molecule whose initial torsion angle is 2.2°. However, when I use the Amorphous Cell module to pack multiple copies of this molecule into a periodic cell, that torsion angle changes. I confirmed this by extracting a single molecule from the .xtd file, and measuring its dihedral. I’ve tried various options, but can’t preserve the 2.2° torsion during packing or the subsequent geometry optimization. My goal is to lock this torsion angle in both the Amorphous
Which RDF curve represents NH–O(water) interaction in polymer–water system?
Dear All, I calculated the RDF between the NH group in my polymer and the oxygen atom in water using MS. The RDF output shows three curves: Total NH, Total WO, and Total NH-WO (as in the screenshot). Which of these should I use to correctly represent the RDF between the polymer NH group and water oxygen atoms? Thanks Hakkim
Adsorption locator module for polymer
Dear All, Can the Adsorption Locator module in Materials Studio be used to identify the adsorption sites of a polymer for a gas molecule like CO₂? If so, is it sufficient to use a single polymer chain in the model, or is it necessary to include multiple chains (e.g., an amorphous cell) to obtain meaningful adsorption site information?. Thanks Hakkim
I use MS to do polymer work, how to calculate the polarizability of repeating units, molecular chains, or aggregation states,
how to calculate the polarizability of repeating units, molecular chains, or aggregation states,
Optimisation of clay structures
Hello everyone, I'm an MS Windows user and I'm having problems. I want to adsorb (molecular dynamics) molecules onto clay surfaces, to do this I've optimised the surfaces (kaolinite and montmorillonite that I've imported onto AMCSD) with CASTEP and Dmol3 but they don't converge. After a few days, the calculation stopped. I just repeat the procedure with the convergence criteria from the articles but still no convergence. Any help would be greatly appreciated. Yours sincerely
the use of Walden’s rule
Hello everyone, I'm working on incorporating the temperature dependency of Gibbs free energy into the QSPR method using Walden’s rule. However, I have some questions regarding the “Dcpfus_estimate” keyword mentioned in the documentation: How do I activate this procedure? Is it as simple as clicking on the check mark in Fig. 1? Is the default entropy change set to 0.0135 kcal/mol·K? If so, do I need to enter this value manually in the interface? Thanks a lot for your assistance! Best regards,
Problem for calculation of rare earth elements solubility in solvents using COSMOTherm
Hello, i uses COSMOtherm for the calculation of the solubility of Neodynium cation (Nd3+) in water and organic solvents. I'm trying to measure the solubility of the NdCl3 salt in different solvents such as water/ methanol/ ethanol. To define the salt I fill "enthalpy of fusion" and "melting point temperature" from litterature. Then i also trying to do tests with deep eutectic solvants (DES). For this i used the ‘multiple solvents’. By defining the solute as an Nd3+ and 3 Cl- salt and entering
cohesive energy density
Hello I got this error after calculating the cohesive energy density. The number of steps in this simulation is 6581700. What should I do to solve this problem? The last ensemble used is NVT.
Criteria for Identifying Non-Covalent Interactions (π–π, cation–π, π–alkyl, etc.) in Protein–Ligand Complexes
Hi everyone, I’m analyzing protein–ligand interactions and used Discovery Studio Visualizer (DSV) to identify various non-covalent interactions, such as π–π stacking, cation–π, and π–alkyl interactions. I would like to understand how these interactions are calculated in structural terms. For example, in the case of π–π stacking, are there specific distance and angular criteria (e.g., centroid–centroid distance between aromatic rings and the angle between their normal vectors) that are typically
Enthalpy of vaporization
Hello, I want to find the enthalpy of vaporization and obtain the CED. Can anyone help?
Issue with COSMO File for ZnCl2 in COSMO-RS
Hi, I have created a COSMO file for ZnCl2 using the TVZPD-fine and TVZP levels of energy in TmoleX multiple times. However, whenever I use this compound in COSMO-RS, I encounter the following error. "CtJob_9.out:38:WARNING: element unknown or not parameterized: ZnCl2 " Could there be something wrong with my COSMO file? Should I generate the COSMO file differently?
the statement in BIOVIA COSMOtherm 2025 ● Reference ManualPage 112 of 389
"The solubility of a solute j in a solvent or solvent mixture i is calculated" subscript “j" should be replaced by "i" ?
Find Pattern tool
Dear All, My system has 3 species, let's say A, B, and C. In the last frame of the dynamics run, I want to delete all the molecules of a particular species (say A) only. Hence, to do this, I am using the Find Pattern tool. But when I am selecting a single molecule of that species from an .xsd file and making that as my pattern document, I am getting this as an error. Can somebody help me get rid of this error? Or is there another way to delete all the molecules of a particular species.
Calculating the total energy of a system in DMol3 under COSMO effects?
Hello Community! I am new to DMol3 and currently optimizing my system under the COSMO effect along with dispersion correction. In the output file (.outmol), I obtained the following energy terms: " Energy components: Sum of atomic energies = -340.5930383Ha Kinetic = -17.9609462Ha Electrostatic = 5.6739496Ha Exchange-correlation = 0.8452897Ha Nonlocal-exchange = 9.5364448Ha Spin polarization = -22.2633431Ha DFT-D correction = -0.0181104Ha
Polymers & Macromolecules
Hi everyone, When we open a COSMO file of a macromolecule, such as a polymer (which it is represented as an oligomer with a limited number of monomer units) in COSMOtherm——should we add information under the polymer properties section from pure compound properties? If so, should properties like density, molecular weight, molar volume, etc., be based on the actual polymer rather than the oligomer used in the simulation?
Can't select atoms by clicking on them
I recently installed Materials Studio and it has never worked properly. I can open the software and it mostly works, but I am unable to select atoms by clicking on them or by using the selection box (click + drag). I have tried every different display style (for ball and stick it will select something that's not the atom I clicked, for the other styles I can't select by clicking at all), and I toggled the 3 checkboxes under tools-options-graphics with no luck. I have tried restarting the program
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Forcite Geometry Optimization
Dear All, When I run Forcite Geometry Optimization, the software plots a graph with the name "Convergence.xcd" . It has two plots inside it namely; Energy Change (kcal/mol) and Grad. Norm (kcal/mol/Angstorm). Can somebody tell me what these two plots exactly mean and how can they be used to judge if my geometry optimization step is correct?