[gmx-users] deformation in simulation

[RAHUL SURESH]

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*