[gmx-users] deformation in simulation

[Tasneem Kausar]

You should apply periodic boundary condition on your protein.
check gmx trjconv -h and selcet (-pbc whole)

First load protein.gro file in vmd. In vmd main window molecule information
is given. Write click on that and then click load data into molecule
option. Select protein.xtc file. It will load the trajectory of protein
snapshots.

On Thu, Feb 23, 2017 at 2:42 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> 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*
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