[gmx-users] deformation in simulation

[RAHUL SURESH]

Dear Amir

Only pdb files are being displayed in vmd
Xtc files are there. They run but there s no display

I have simulated






On Thu, 23 Feb 2017 at 1:43 PM, Amir Zeb <zebamir85 at gmail.com> wrote:

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