[gmx-users] deformation in simulation

[RAHUL SURESH]

I am just doing my production run. I don't get any satisfactory conformer.



On Thu, Feb 23, 2017 at 1:21 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*