[gmx-users] Protein fragments during production simulation
sapnauser365 at gmail.com
Wed Apr 29 07:16:22 CEST 2015
Thank your for your help. I could get over the issue. :)
On Tue, Apr 28, 2015 at 11:44 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> Hi Sapna,
> On Apr 28, 2015 6:26 AM, "SAPNA BORAH" <sapnauser365 at gmail.com> wrote:
> > Dear all,
> > I am trying to simulate a globular protein predicted by Ab-initio method
> > using web servers, Robetta and Itasser. I am currently using Gromacs
> > A problem has occured during the production md run, when my protein
> > to break into fragments while it remains inside the water box.
> > Energy minimisation is achieved in 15000 steps using steep gradient.
> > Equilibration is run for 1ns.
> > Production md is run for 100ns.
> > My complete mdp file for production run in as follows:
> > ------run.mdp------
> > integrator = md
> > nsteps = 50000000
> > dt = 0.002
> > nstlist = 10
> > rlist = 1.0
> > coulombtype = pme
> > rcoulomb = 1.0
> > cutoff-scheme = verlet
> > vdw-type = cut-off
> > rvdw = 1.0
> > tcoupl = v-rescale
> > tc-grps = protein non-protein
> > tau-t = 0.1 0.1
> > ref-t = 298 298
> > nstxtcout = 1000
> > nstenergy = 1000
> > constraints = all-bonds
> > ------------------
> > Can you please help me with the issue?
> > Thanking You.
> > Regards,
> > Sapna Mayuri Borah
> > Research Student
> > Tezpur University
> > India
> > --
> > 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-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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-request at gromacs.org.
Sapna Mayuri Borah
More information about the gromacs.org_gmx-users