[gmx-users] deformation in simulation

[RAHUL SURESH]

Okay thank you
On Thu, 23 Feb 2017 at 3:14 PM, Tasneem Kausar <tasneemkausar12 at gmail.com>
wrote:

> here is whole command
> gmx trjconv -f production.xtc -s protein.tpr -o production_pbc.xtc -pbc
> whole
>
> On Thu, Feb 23, 2017 at 3:13 PM, Tasneem Kausar <tasneemkausar12 at gmail.com
> >
> wrote:
>
> > 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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*