Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

Hi Carsten, Thanks for your reply. Actually I am running MD simulation on a protein molecule with 270 residues(2687 atoms), after adding water it is having 45599 atoms, and using the recent version of gromacs test available from gromacs.org (gmxtest-3.3.3.tgz) Following are the entries from the

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

Sorry, I forgot to mention that one cofactor NDP, I added in my molecule using PRODRG server. 2008/9/12 vivek sharma [EMAIL PROTECTED] Hi Carsten, Thanks for your reply. Actually I am running MD simulation on a protein molecule with 270 residues(2687 atoms), after adding water it is having

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

Hi Vivek, I think I'm a bit lost now. We were originally talking about differences in trajectories but from the mail you just sent I can see that you have a segmentation fault, which is another problem. I can only suggest that if you want to make use of 128 processors you should download the

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

HI Carsten, Thanks again for reply. and my apologies for putting question out of discussion. actually I tried same command with -np 24 and -np 64, and for both cases i got different trajectory (while analyzing them using ngmx). Also Can you suggest me some tutorial or reference to get details of

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

vivek sharma wrote: HI Carsten, Thanks again for reply. and my apologies for putting question out of discussion. actually I tried same command with -np 24 and -np 64, and for both cases i got different trajectory (while analyzing them using ngmx). If you look at a plot of your data, e.g.

[gmx-users] Gromacs parellal run:: getting difference in two trajectories

Hi There, I am running gromacs parellal version on cluster, with different -np options. On analyzing the 5 nsec trajectory using ngmx, I am finding difference in the trajectory of two similar runs (only thing varying in two runs in -np i.e 20 and 64 ), where mdp file and input files are same in

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

vivek sharma wrote: Hi There, I am running gromacs parellal version on cluster, with different -np options. On analyzing the 5 nsec trajectory using ngmx, I am finding difference in the trajectory of two similar runs (only thing varying in two runs in -np i.e 20 and 64 ), where mdp file and

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

vivek sharma wrote: Hi There, I am running gromacs parellal version on cluster, with different -np options. Hi, which version of gromacs exactly are you using? On analyzing the 5 nsec trajectory using ngmx, I am finding difference in the trajectory of two similar runs (only thing varying in

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

Thanks david for your reply. Can you tell me up to how many -np value current version of GROMACS can be optimized (or will reduce the simulation time) ? Also, how can I test the accuracy of my process when I can't get same result with similar option (while scaling )? With Thanks, Vivek