[gmx-users] deformation in simulation
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
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
gromacs.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users
More information about the gromacs.org_gmx-users