Hi, After applying energy minimization most of the atoms leave the box ( around 95%).
I am using a composite system of polymer and clay. The composite box (5.8 nm * 5.8 nm *7 nm) is made from combining a polymer box (5.7 nm * 5.7 nm * 5.7 nm) and clay box (5.5 nm * 5.1 nm * 1 nm) using editconf and genbox. I am not using any solvent in the system. Could that create a problem? Or could the problem be that the box dimensions are too small? In that case should I increase the size of the composite box. Also, If I increase the size of the box how do I ensure that the density of the system does not chance. Thanks for your help. ------------------------------ > > Message: 3 > Date: Thu, 4 Apr 2013 14:05:31 +0800 (CST) > From: "song.yongshun" <song.yongs...@163.com> > Subject: Re:[gmx-users] Applying periodic boundary conditions in > energy minimization > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: > <48b65938.13820.13dd3a668a3.coremail.song.yongs...@163.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > Actually you have already applied pbc,and there seems nothing wrong. > Some atoms are out of the box is common. > If your box vector is correct,then Gromacs will run successfuly afterwards. > At 2013-04-03 22:51:54,"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 > -- 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