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

Vedat Durmaz durmaz at zib.de
Thu Sep 7 16:29:54 CEST 2017

i really appreciate this pretty informative answer. and do you also know, what the infix "n254" or "n2" stands for?

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?


Am 07.09.2017 um 14:26 schrieb Justin Lemkul:
> On 9/6/17 5:55 AM, Vedat Durmaz wrote:
>> hi guys,
>> from time to time i'm faced with GMX output files during MD called, e.g. in the current case:
>> step8164372b_n254.pdb
>> step8164372b_n2.pdb
>> step8164372c_n254.pdb
>> step8164372c_n2.pdb
>> what i know is that they are related to kind of exploding systems. however, i'm not really able to interpret their content. if i visualize them in VMD, i see a subset of my system surounded by explicit water molecules where the two *n254* files contain a larger part of my fibrils (polypeptides) than the *n2* files which only show few atoms of one particular amino acid. but if i pick certain atoms of the amino acids, they are often not correctly assigned to residue names and the atom index shown in VMD is different from the index listed in the underlying gro file.
>> where can i find detailed information about how to interpret the names and contents of these files? why are exactly these atoms written to the pdb files and what does the file name tell me?
> These files contain the atoms in a given domain (e.g. on a certain CPU 
> core) and are before (b) and after (c) applying constraints of a given 
> step.  I personally have never found them to be useful in determining 
> anything, but they are an indicator of physical instability.
> -Justin

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