Dear DS users and Moderators,

Good Morning !!!

I am running Protein-inhibitor complex simulations using CHARMm force field in DS 2.1. I have no problem in minimization and Solvation with default counter ions steps. After these two steps, I ran the Production step using Standard Dynamics Cascade. After 25 hours, The Job gets error. I tried many times still the problem is same. When I reduced the Production steps in Production of Standard Dynamics Cascade, sometimes the job is successful. However, the job gets error in the subsequent Dynamics production. To know the error, I took a look at CHARMm and Output log files. The error message from output log file is as below.

“CHARMm dynamics simulation has failed because energy change tolerance exceeded. Please ensure the initial structure is minimized and parameters such as step size are reasonable (e.g. for many systems no greater than 0.001 ps).

[2010-07-15 10:21:46] [ERROR] CHARMm Simulation has failed [2010-07-15 10:21:46] Client message: 'CHARMm Simulation has failed'

I am not able to understand the “energy change tolerance exceeded” and “Please ensure the initial structure is minimized and parameters such as step size are reasonable (e.g. for many systems no greater than 0.001 ps)”. I minimized the initial structure with 5000 steps of Steepest Decent and 10000 steps of Conjugate Gradient with heavy atom constraints. Moreover, in the Standard Dynamics Cascade, I used the heavy atom constraints in the first two minimization steps and in heating but not in Equilibration and production steps.

I have attached my simulation protocol, .rst file, and CHARMm log file and Output log file  for details.

Thank you very much in advance

Sincerely,

Malai