[gmx-users] HPC performance in Gromacs ?

Thanks, Pall, I thought more threads will make the simulation faster. Is it not the case for Gromacs? I have tried to change the values. The file is provided here, https://drive.google.com/a/rug.nl/file/d/0B-VoMAn-UrjYeko4d1VwUURCb00/view?usp=sharing . The command line is "gmx_mpi_d mdrun -s

[gmx-users] HPC performance in Gromacs ?

Hello Nikhil, Thanks for your suggestions. here is the links for two log files. 1 is for normal set, 2 is for tunning set. https://drive.google.com/a/rug.nl/file/d/0B-VoMAn-UrjYbEY2dUFvS3pLUWs/view?usp=sharing https://drive.google.com/a/rug.nl/file/d/0B-VoMAn-UrjYcjctSHBOckRKeEU/view?usp=sharing

[gmx-users] HPC performance in Gromacs ?

Hello all, I have a report as following, but I do not have any clear clue about what I have to do. If I change some default values for -dd/-dds/..., what I should expect and what I should be careful about about tunning these parameters? It said the load imbalance is from inhomogeneous. But I am

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 156, Issue 48

Hello, Justin, You were correct about the simulation box. I calculated the simulation box again. I found the volume should be smaller just as your suggestion. And now it works. But I had found a question when I tried to find out how the memory was allocated before I changed the box size. The

[gmx-users] Error during nvt: Not enough memory. Failed to allocate 3425307227 aligned elements of size 4 for grid->grid. What is happening

This error appeared when I tried to do a NVT simulation. The simulation box is 768.0 768.0 768.0 [nm**3], in which there are 9 atoms. The force-field is OPLSAA. I attached the md parameter file for this simulation. Hope someone who can help me find the problem. Thanks in advance.