[gmx-users] deformation in simulation

[Tasneem Kausar]

here is whole command
gmx trjconv -f production.xtc -s protein.tpr -o production_pbc.xtc -pbc
whole

On Thu, Feb 23, 2017 at 3:13 PM, Tasneem Kausar <tasneemkausar12 at gmail.com>
wrote:

> You should apply periodic boundary condition on your protein.
> check gmx trjconv -h and selcet (-pbc whole)
>
> First load protein.gro file in vmd. In vmd main window molecule
> information is given. Write click on that and then click load data into
> molecule option. Select protein.xtc file. It will load the trajectory of
> protein snapshots.
>
> On Thu, Feb 23, 2017 at 2:42 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
>> Dear Amir
>>
>> Only pdb files are being displayed in vmd
>> Xtc files are there. They run but there s no display
>>
>> I have simulated
>>
>>
>>
>>
>>
>>
>> On Thu, 23 Feb 2017 at 1:43 PM, Amir Zeb <zebamir85 at gmail.com> wrote:
>>
>> > first you let me know, you have produced your md run or not?
>> > xtc file is the output of md production, if you didn't actually simulate
>> > yet, how can you get xtc file?
>> >
>> > On Thu, Feb 23, 2017 at 12:07 AM, RAHUL SURESH <drrahulsuresh at gmail.com
>> >
>> > wrote:
>> >
>> > > again why XTC files are not being displayed in vmd
>> > > ?
>> > >
>> > >
>> > > On Thu, Feb 23, 2017 at 1:34 PM, Amir Zeb <zebamir85 at gmail.com>
>> wrote:
>> > >
>> > > > so what did you find?
>> > > > Did you fix the problem?
>> > > >
>> > > > On Wed, Feb 22, 2017 at 11:51 PM, Subashini .K <
>> subashinik at hotmail.com
>> > >
>> > > > wrote:
>> > > >
>> > > > > Many tutorials suggest to run two equilibrations and then
>> production
>> > > > file.
>> > > > >
>> > > > >
>> > > > > At first, run a restrained equilibrium.
>> > > > >
>> > > > >
>> > > > > Then non-restrained equilibrium followed by production file.
>> > > > >
>> > > > >
>> > > > > Do not know the aim of your simulations.
>> > > > >
>> > > > >
>> > > > > Hope this answer helps.
>> > > > >
>> > > > >
>> > > > > Thanks,
>> > > > >
>> > > > > Subashini.K
>> > > > >
>> > > > > ________________________________
>> > > > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>> > > > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
>> > RAHUL
>> > > > > SURESH <drrahulsuresh at gmail.com>
>> > > > > Sent: Thursday, February 23, 2017 12:23 PM
>> > > > > To: gmx-users at gromacs.org
>> > > > > Subject: [gmx-users] deformation in simulation
>> > > > >
>> > > > > 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*
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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>
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