[gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????

[himanshu khandelia]

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.

Here are the commands that were used:

DESHUFFLING
1. trjconv -s ../DYNA-NVT/popc-big-3.tpr -f popc-big-3.gro -n
../DYNA-NVT/deshuf.ndx -o popc-dyna-3-deshuf.gro
2. trjconv -s ../DYNA-NVT/popc-big-3.tpr -f popc-big-3.trr -n
../DYNA-NVT/deshuf.ndx -o popc-dyna-3-deshuf.trr

NPT SETUP AND RUN:
For 4 cpus:
3. grompp -sort -shuffle -np 4 -f dyna-npt.mdp -c
popc-dyna-3-deshuf.gro -p large.top -o popc-big-4.tpr -t
popc-dyna-3-deshuf.trr > & log
4. mpirun -np 4 ~/gromacs-3.3.1/bin/mdrun_mpi -v -s popc-big-4.tpr -o
temp.trr -c temp.gro -e temp -g temp.log > & temp.out

For 1 cpu:
3. grompp -f dyna-npt.mdp -c popc-dyna-3-deshuf.gro -p large.top -o
popc-big-4.tpr -t popc-dyna-3-deshuf.trr > & log
4. ~/gromacs-3.3.1/bin/mdrun -v -s popc-big-4.tpr -o temp.trr -c
temp.gro -e temp -g temp.log > & temp.out