Hi,

I am running some simulations of polymers with drug molecules in water in Materials Studio using Discover module. I am having serious problems using thermostats/barostats in MD calculations as noted below.

I know that Berendsen thermostats and barostats are good to use during equilibration and Nose Hoover thermostat + Parrinello Rahman barostat are good for production. However, even after a long equilibration (~5ns) on a small system (~3nm box size), the system does not reach the reference temperature of 298 K if I use the Nose Hoover+Parrinello Rahman. Below is a fragment of the output for production. I understand why the pressure fluctuations are large for small system (my reference pressure is 0.0001 GPa=1bar) but the temperature should go to 298K. If I use Berendsen thermostats and barostats for production as well, the density values keep falling and go less than 1 g/cc, Nose Hoover+Parrinello Rahman seem to give reasonable density values for my system. Any inputs on why is this happening?

Regards,

Prateek

(This is the first post in the forum so please let me know if I am adhering to any forum rules)

MOLECULAR DYNAMICS

__________________

Ensemble           :       NPT

Temperature        :    298.00 K

Control Method     :   Nose, Q =  18443577.60 kcal/mol*fs^2

Pressure           :    0.0000 GPa

Stress             : Sxx =   -0.0001 GPa Syy =   -0.0001 GPa Szz =   -0.0001 GPa

                   : Syz =    0.0000 GPa Sxz =    0.0000 GPa Sxy =    0.0000 GPa

Control Method     : Parrinello, cell mass =        20.00 a.m.u.

Timestep           :      1.00 fs

Duration           :3000000.00 fs

Integration Method : Velocity Verlet

Initial Velocities :   Random Velocities from Boltzmann distribution

Initial Temp.      :    298.00 K

Dynamics Summary

________________

    Initial        Final      Average    Std. Dev.

    -------        -----      -------    --------- 

Tot. energy (kcal/mol)     -747.765     -737.965     -914.051       94.996

Pot. energy (kcal/mol)    -2383.205    -2266.891    -2424.024       84.996

Kin. energy (kcal/mol)     1635.440     1528.927     1509.973       37.018

Temperature (K)             298.000      278.592      275.138        6.745

Pressure (GPa)            -0.031331    -0.013400    -0.031288     0.149142

Volume (A^3)              19449.049    18957.028    18677.540      194.104

Density (gm/cm^3)            1.1347       1.1642       1.1817       0.0123

Time used by 3000000 steps is 34 hours 27 mins 25.28 secs (0.041 secs per step)