[gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????
hkhandelia at gmail.com
Sat Oct 27 09:40:15 CEST 2007
Thanks for the reply. But why the difference between the 4-cpu and the 1-cpu ?
On 10/27/07, Mark Abraham <mark.abraham at anu.edu.au> 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.
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