[gmx-users] deformation in simulation

[Amir Zeb]

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*
> --
> Gromacs Users mailing list
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