[gmx-users] deformation in simulation

[Amir Zeb]

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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> >> > > > *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*
> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
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