[gmx-users] numbering of .gro file

Anna Marabotti anna.marabotti at isa.cnr.it
Fri May 13 14:09:42 CEST 2011

Dear gmx-users,
I'm simulating a homodimeric protein obtained by homology modelling. In the
.pdb file, I have 2 chain identifiers (A and B). I used Gromacs 4.0.7 to
prepare the .gro files for simulation (up to nvt); then I was forced to
switch to Gromacs 4.5.4 on another machine to continue with npt and full MD.
I used the files from Gromacs 4.0.7 to continue, and it seems to me that all
went OK. Now I have the files from the full MD, and I started to analyze
I used g_rmsf to analyze the fluctuations of the residues, and I found that
the results for the two subunits of the protein are superimposed. In the
file .gro that comes from the MD as well as in the file .gro that comes from
the npt MD made with Gromacs 4.5.4, the number of residues of the second
subunit does not continue after the first subunit (i.e. after the last 359th
residue of the first subunit, I see that the first residue of the second
subunit is numbered 1 instead of 360), but in the nvt file produced by
Gromacs 4.0.7 that I provided to Gromacs 4.5.4, the numbering of the two
subunits is sequential. 
My questions are:
1) why Gromacs 4.5.4 changed the numbering of the residues in the two
subunits, even if it started from a .gro file?
2) Does this affect the result of the MD?
3) how can I separate, or renumber, the resulting .gro files in order to
have a graph in which the fluctuations are not superimposed?
Thank you very much and regards
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabotti at isa.cnr.it
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
(Roberto Benigni, about Roberto Saviano)
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