Hi Nitu, Energy minimization is only to remove some strain from your system. You probably don't want to include position restraints there. After energy minimization you typically run a short MD run in which you use position restraints such that the protein/DNA doesn't move to much, but the water can equilibrrate with respect to the protein. Check the tutorial material linked on the wiki. This stuff is mentioned in all of them.
Cheers, Tsjerk On Wed, Jul 1, 2009 at 2:06 PM, nitu sharma<sharmanit...@gmail.com> wrote: > Dear Tsjerk > > Thanks for your right suggestion. It works successfully > for dna-protein complex simulation. i want to ask one more thing , can I use > parameter file for energy minimisation which i have used for membrane > protein simulation or can u suggest me what changes I have to make in > parameter file to use for dna- protein complex simulation. > the parameter file like this- > cpp = /usr/bin/cpp > define = -DPOSRE_PROTEIN > constraints = none > integrator = steep > dt = 0.002 > nsteps = 10000 > ; > ; Energy minimizing stuff > ; > emtol = 1000 > emstep = 0.0001 > > nstcomm = 1 > nstlist = 10 > ns_type = grid > rlist = 1.0 > rcoulomb = 1.0 > vdw-type = cut-off > rvdw = 1.0 > coulombtype = PME > Tcoupl = no > Pcoupl = no > gen_vel = no > comm-mode = Linear > pbc = XYZ > > Specially where i have apply position restrain? > > Thanking you > Nitu sharma > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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/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/mailing_lists/users.php
