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

Justin Lemkul jalemkul at vt.edu
Sun Jan 6 06:45:43 CET 2013

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


More information about the gromacs.org_gmx-users mailing list