[gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Jan 6 07:00:20 CET 2013

I ran NPT equilibration for 1ns. Would that be ok if I rerun it for 1 or more ns ?


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, January 6, 2013 9:15 AM
Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

On 1/6/13 12:33 AM, Shima Arasteh wrote:
> Do you mean that I re-run NPT step with the new index file and npt.gro (which I got from the last NPT equilibration)? That's not clear to me yet.

That's where I'd start.  You may have to run the new configuration through the entire equilibration protocol, though.  Instability during MD often indicates inadequate equilibration, so whatever your protocol is may not be sufficient as is and may require greater time.


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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