[gmx-users] deformation in simulation

[RAHUL SURESH]

I have generated my index file now using make_ndx command

On Thu, Feb 23, 2017 at 1:18 PM, Amir Zeb <zebamir85 at gmail.com> wrote:

> Hello,
>
> You would have xxx.xtc file. actually, this is your xtc file what ever the
> name you have given, just put your corresponding xtc file therein.
> Once you are directed to prompt option, you should select 0 "system"
>
>
>
> On Wed, Feb 22, 2017 at 11:39 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
> > Also I dont have traj.xtc file.
> >
> > On Thu, Feb 23, 2017 at 1:03 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> > > 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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> > >> > > > *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*
> > >
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*