Thanks for the reply. But why the difference between the 4-cpu and the 1-cpu ?
On 10/27/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > Hi > > > > I seem to be doing something wrong here, but cannot figure out what. > > > > - I have run a 200 ps NVT simulation for a lipid bilayer on 4 > > processors using the gromacs-3.3.1 build. > > > > - The last frame from the NVT simulation was used in conjunction with > > a newly written .mdp file to restart the simulation using grompp. > > (Before doing this, the trajectory and the final .gro file were > > deshuffled). > > > > - When the NPT .tpr is built for 4 processors (using -shuffle and > > -sort), the NPT simulation immediately explodes perhaps because the > > density is high (1100 kg/m3). However, if the NPT .tpr is built for a > > single cpu, then the simulation does not immediately explode, and has > > run now for at least 3000 steps. (the .edr file from NVT was not > > used). The same mdp file was used to generate both the 4-cpu tpr and > > the 1-cpu tpr. > > > > Why should this happen ??? I am hoping I have made some mistake here. > > Numerical simulations do that when you shift to an ensemble where the > present structure is far enough from equilbrium. Try a gentler tau_p > and/or position restraints on your solute. > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
