After adding water you can do energy minimization (EM) in two steps: 1. Constrain the protein backbone and do EM. 2. Now do EM on the full system. 3. Run a short MD simulation by constraining the protein backbone. The above three steps will help hydrate the protein molecule with minimal distortion of protein structure.
4. Now run a MD on full system. for details looks here: http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ -Gaurav On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal < sonali11dhind...@yahoo.co.in> wrote: > Sorry, but I couldnt get your question, > I have used this .mdp file for energy minimisation after addition of water > and using > > GROMOS96 43a1 force field : > > > title = drg_trp > cpp = /lib/cpp ; location of cpp on SGI > define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] > constraints = none > integrator = steep > dt = 0.002 ; ps ! > nsteps = 2000 > nstlist = 10 > ns_type = grid > rlist = 0.9 > coulombtype = PME ; Use particle-mesh ewald > rcoulomb = 0.9 > rvdw = 1.0 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > ; > ; Energy minimizing stuff > ; > emtol = 1000.0 > emstep = 0.01 > > I hope it will help you to guide me further > Thanks > -- > Sonali Dhindwal > > > --- On *Wed, 19/5/10, Erik Marklund <er...@xray.bmc.uu.se>* wrote: > > > From: Erik Marklund <er...@xray.bmc.uu.se> > Subject: Re: [gmx-users] enegry minimisation > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Wednesday, 19 May, 2010, 5:31 PM > > > sonali dhindwal skrev: > > Hello All > > This question may sound trivial to many, but as i am new to this field, > please help. > > I want to ask a question regarding my previous query of distortion of > protein strucutre after molecular dynamcs simulation. > > I have noticed that after enegry minimisation using steepest decent > algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion > occurs. > > So is it necessary to do enegry minimisation step before MD, because this > is my modeled protein, and i have already done energy minimisation using > different program and after that I have done refinement also. > > Thanks and regards > > ^ > > > > > > -- > > Sonali Dhindwal > > > > > So how has your system setup changed since your previous EM? Addition of > water? Cutoffs? PME? > > -- ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se <http://mc/compose?to=er...@xray.bmc.uu.se> > http://folding.bmc.uu.se/ > > -- gmx-users mailing list > gmx-users@gromacs.org<http://mc/compose?to=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<http://mc/compose?to=gmx-users-requ...@gromacs.org> > . > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > 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 >
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