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

[Vytautas Rakeviius]

Energy minimization output explains them. I do not think they are important if you get good energy minimization after all.
 

    On Thursday, September 7, 2017, 3:41:59 AM GMT+3, Vedat Durmaz <durmaz at zib.de> 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?

any hint is appreciated.

many thanks,

vedat durmaz


-- 
Vedat Durmaz
Computational Molecular Design
Zuse Institute Berlin (ZIB)
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14195 Berlin, Germany
T: +49-30-84185-139
F: +49-30-84185-107
http://www.zib.de/durmaz

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