[gmx-users] deformation in simulation

[RAHUL SURESH]

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*