Hello Robert and Peter,

The script builder works fine now and warns about the problem.

Thanks for all your help.

-Krishnadev

Hi Peter,

Thanks a lot for the help. I had not realized that Barostat was still on even in the implicit solvent simulations. Removing it resolved the problem. Perhaps, the script builder can be modified to warn about this scenario.

Thanks,
Krishnadev

Hello Peter, I tried with time steps of 0.5fs, 1.0fs and 2.0fs with friction terms of 1.0/ps and 2.0/ps. But it kept crashing randomly. But, if I increase the equilibration from 100 steps to 1000 steps, then the simulation completes 100000 steps of production run without problem even with the origin...

Hello, I am trying to simulate a protein (based on 1mq4, 272 residues) with OpenMM 5.1 compiled from source (compilation gave no errors, and all CUDA tests passed). Hardware specs are dual X5560 CPU and a GTX670 with system memory of 24GB. My system is running Ubuntu 12.04 and I have python 2.7.3, C...