[gmx-users] deformation in simulation

[Amir Zeb]

alright
you first centralize your system by the following command
trjconv -f traj.xtc -s md.tpr -n index.ndx -o md.xtc -pbc mol -ur compact
and then visualize
probably you would have solved it. This is some how visualization  problem.

On Wed, Feb 22, 2017 at 11:06 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> using VMD
>
> On Thu, Feb 23, 2017 at 12:32 PM, Amir Zeb <zebamir85 at gmail.com> wrote:
>
> > how do you visualize your system structure?
> >
> > On Wed, Feb 22, 2017 at 10:58 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> > > Dear amir
> > >
> > > They are forming long bonds. I hope you understand what i mean. Like
> few
> > > molecules move away from the protein still bonded. and they again
> > converge
> > > at some point but again they do deform.
> > >
> > >
> > >
> > > On Thu, Feb 23, 2017 at 12:26 PM, Amir Zeb <zebamir85 at gmail.com>
> wrote:
> > >
> > > > Hey
> > > > I don't know very well about the problem you have.
> > > > Did you minimize your system well converged?
> > > > You may go for conjugate minimization
> > > >
> > > > All the best!
> > > >
> > > > On Wed, Feb 22, 2017 at 10:53 PM, RAHUL SURESH <
> > drrahulsuresh at gmail.com>
> > > > wrote:
> > > >
> > > > > 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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> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
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> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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