[gmx-users] deformation in simulation

[Amir Zeb]

first you let me know, you have produced your md run or not?
xtc file is the output of md production, if you didn't actually simulate
yet, how can you get xtc file?

On Thu, Feb 23, 2017 at 12:07 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

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