I have a clay pdb file http://s24.postimg.org/je3mvov9h/MMT.png
and a polymer structure file: http://s24.postimg.org/ei003zv45/PLA.png I use the following commands to generate a composite box > genbox -cp mmt.pdb -o mmt_box.gro > editconf -f mmt_box.gro -o mmt_newbox.gro -box 5.800 5.811 7.5 -center 2.499 2.658 0.647 > genbox -cp pla.gro -o pla_box.gro > editconf -f pla_box.gro -o pla_newbox.gro -box 5.800 5.811 7.5 -center 2.732 2.722 4.277 > genbox -cp mmt_newbox.gro -ci pla_newbox.gro -nmol 1 -o mmt_pla.gro -try 100 Image of composite box: http://s24.postimg.org/w9g7w6zwl/MMT_PLA.png After this I run the energy minimization using following commands > grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 1 > mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log -nt 1 The structure after energy minimization: http://s24.postimg.org/3l39syxqd/After_EM.png Below are the links for em.mdp, and system.top em.mdp : http://pastebin.com/3YsPR4FX system.top : http://pastebin.com/2PXdPA9P I hope this is everything you require. Thanks for you help. ------------------------------ > > Message: 3 > Date: Thu, 04 Apr 2013 04:14:57 -0400 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Re: Applying periodic boundary conditions in > energy minimization > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <515d3681.30...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 4/3/13 9:46 PM, Abhinav Agrawal 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 > >>> > >>> > >> This last line means PBC are being applied. Your observations are > >> consistent with using a box that is too small for the solute, but since > you > >> haven't supplied information as to (1) what the system is, (2) how you > >> built it, or (3) how large the box is, there's very little to say beyond > >> speculation. > >> > >> -Justin > >> > >> -- > >> > >> ======================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Research Scientist > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) > >> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> ======================================== > >> > > > > 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. > > > > 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. > > > > No, the box size seems reasonable. I only suggested that because the > behavior > you described (unfolding of the polymer) seemed to indicate spurious forces > across PBC. As Tsjerk rightly noted, there's no such thing as "outside" > of an > infinite system. > > Without the exact sequence of commands and links to before and after > images of > the behavior you're seeing, there's not really much anyone can do to help. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- 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