I am just doing my production run. I don't get any satisfactory conformer.
On Thu, Feb 23, 2017 at 1:21 PM, Subashini .K <subashi...@hotmail.com> wrote: > Many tutorials suggest to run two equilibrations and then production file. > > > At first, run a restrained equilibrium. > > > Then non-restrained equilibrium followed by production file. > > > Do not know the aim of your simulations. > > > Hope this answer helps. > > > Thanks, > > Subashini.K > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL > SURESH <drrahulsur...@gmail.com> > Sent: Thursday, February 23, 2017 12:23 PM > To: gmx-us...@gromacs.org > Subject: [gmx-users] deformation in simulation > > Simulating a protein with 100residues for 200ns doesn't show any stability. > There are some deformation(long-bonds) in the structure throughout the > process. Why is that so? Can I choose any stable structure in between these > 200ns, for example say 176ns. Or is there any other way to make them work > good.I need your valuable suggestions > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > gromacs.org_gmx-users Info Page - Royal Institute of ...< > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> > maillist.sys.kth.se > gromacs.org_gmx-users -- Discussion list for GROMACS users About > gromacs.org_gmx-users > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
