[gmx-users] deformation in simulation

[Amir Zeb]

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*
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> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
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