[gmx-users] deformation in simulation

Subashini .K subashinik at hotmail.com
Thu Feb 23 08:57:08 CET 2017

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.



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

*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
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