[gmx-users] purpose of step pdb files during MD

Justin Lemkul jalemkul at vt.edu
Thu Sep 7 21:10:16 CEST 2017

On 9/7/17 10:29 AM, Vedat Durmaz wrote:
> i really appreciate this pretty informative answer. and do you also know, what the infix "n254" or "n2" stands for?

Node ID.

> what i found strange is that the error occurs after nearly 10M MD steps. in other copies of the same system, the error doesn't occur at all even after the entire predefines time span (40ns).
> it's a long fibril chain (>200 repeating units) of a 7mer polypeptide. the walls of the triclinic simulation box of size 10x8x70 nm have an initial distance of 1.5 nm to the fibril and i have chosen "comm-mode  = linear" in order to keep the system centered. i'm actually wondering, whether that might have caused the error or whether the system will for sure crash if the long chain changes its shape to some spheric one that doesn't fit the slim box anymore.
> do you have any experience with that?

Nope, sorry.  A crash after a long simulation time is very unusual and 
hard to diagnose.  Normally things fail rather quickly.  Does your 
GROMACS installation pass all regression tests?




Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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