[gmx-users] Difference in molecule wrapping in gro file

[anu chandra]

Dear Gromacs users,

I just noticed that  the gro file written from simulation carried out in
Dell cluster and my local desktop workstation have difference in warping
the molecules.

 In server, following grommp and mdrun commands are used,

gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n
index.ndx -p topol.top

mpirun -ppn 16 -np 64 gmx_mpi mdrun -deffnm MD5


and the output gro file do not wrap the molecules, i.e I can seen the
surface molecules are broken while visualizing the gro file.

But, the same simulation using following commands generated the gro file
with molecules wrapped well in the box.

gmx grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n
index.ndx -p topol.top

gmx mdrun -nt 8 -deffnm MD5

In both case, mdp file have exactly same parameters and the only difference
was in nsteps.

Can any one help to find out what make this difference in gro file writing?

Many thanks

Anu