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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
