There is no outside of the box. Tsjerk
On Wed, Apr 3, 2013 at 4:51 PM, Abhinav Agrawal <abhv.a...@gmail.com> wrote: > Hi, > > I have a polymer box on which I wish to apply energy minimization. However, > when I do energy minimization runs to polymer chain unravels and goes out > of the box. I guess this is because periodic conditions are not applied. > > My em.mdp file is: > > > > > ; > > cpp = /usr/bin/cpp > > define = -DFLEX_SPC > > constraints = none > > integrator = steep > > nsteps = 1000 > > ; Energy minimizing stuff > > ; > > emtol = 2000 > > emstep = 0.01 > > nstcomm = 1 > > ns_type = grid > > rlist = 1 > > rcoulomb = 1 > > rvdw = 1 > > Tcoupl = no > > Pcoupl = no > > gen_vel = no > > pbc = xyz > > > > I used the following commands: > > grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 2 > > > > > > mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log > > > > Can you please tell me what I am doing wrong. Thanks in advance > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists