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

Vedat Durmaz durmaz at zib.de
Fri Sep 8 10:04:49 CEST 2017

Am 07.09.2017 um 21:10 schrieb Justin Lemkul:
> 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

ok. since i haven't compiled this gromacs installation i haven't seen any results of its test runs. anyway, i carried out the simulations again and this time no error occurred.

thanks again for your help!


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