[gmx-users] deformation in simulation

[RAHUL SURESH]

what is that compact?

And my protein is still within the system.(BOX)

On Thu, Feb 23, 2017 at 12:40 PM, Amir Zeb <zebamir85 at gmail.com> wrote:

> 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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> > > > *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*