[gmx-users] deformation in simulation

[RAHUL SURESH]

again why XTC files are not being displayed in vmd
?


On Thu, Feb 23, 2017 at 1:34 PM, Amir Zeb <zebamir85 at gmail.com> wrote:

> so what did you find?
> Did you fix the problem?
>
> On Wed, Feb 22, 2017 at 11:51 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.
> >
> --
> 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*