[gmx-users] deformation in simulation

[Subashini .K]

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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