[gmx-users] NVT equilibration

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Thu Aug 9 14:30:04 CEST 2012

Are you running NVT with position restraint dynamics of your protein?
Your system is probably not minimizied enough.


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Shima Arasteh [shima_arasteh2001 at yahoo.com]
Sent: Thursday, August 09, 2012 1:23 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] NVT equilibration

Dear gmx users,

I used the NVT (T=300) equilibration for my system ( a protein in water). The first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96 with an average temperature around 299.803 K.

Then I though of a better convergence, so set the equilibration to 200 ps. But it stopped due to some error:
Fatal error:
1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.

I'd like to know why such an error might happen? Is a shorter equilibration better for NVT generally?

gmx-users mailing list    gmx-users at gromacs.org
* Only plain text messages are allowed!
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list