[gmx-users] deformation in simulation

[RAHUL SURESH]

Dear Amir

Its done
Thank you..
Its working

On Thu, Feb 23, 2017 at 1:39 PM, Amir Zeb <zebamir85 at gmail.com> wrote:

> means that you didn't produce your simulation run yet?
>
> On Thu, Feb 23, 2017 at 12:06 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
> > 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 <subashinik at 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-bounces at maillist.sys.kth.se <
> > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of RAHUL
> > > SURESH <drrahulsuresh at gmail.com>
> > > Sent: Thursday, February 23, 2017 12:23 PM
> > > To: gmx-users at 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-request at 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-request at 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-request at gromacs.org.
> >
> --
> 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.
>



-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*