> > 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. -- 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