[gmx-users] deformation in simulation

[RAHUL SURESH]

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