R: Re: [gmx-users] numbering of .gro file

Anna Marabotti anna.marabotti at isa.cnr.it
Fri May 13 14:41:44 CEST 2011

Dear Justin,
thank you very much for infos. I was aware that in Gromacs 4.5.4 pdb2gmx
does not renumber the PDF file anymore; what seems strange to me is that
Gromacs 4.5.4 "backnumbered" also a .gro file that was already renumbered by
4.0.7, without using pdb2gmx (I only took the nvt.gro and nvt.trr files
obtained by version 4.0.7 and grompp'ed them using version 4.5.4 to obtain
the npt.tpr file to continue with npt simulation).
However, thank you very much for suggestion and best regards

Date: Fri, 13 May 2011 08:30:41 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] numbering of .gro file
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DCD2471.3020801 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anna Marabotti wrote:
> 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 them.
> 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?

The behavior in 4.0.7 was for pdb2gmx to always renumber the input
file so that your resulting, processed coordinates started with residue 1
proceeded sequentially.  For various reasons, people did not always want
so in 4.5 the -renum flag was added and the default behavior was changed so
renumbering did not occur unless requested, and each chain was numbered 
independently of any previous chain.

> 2) Does this affect the result of the MD?

Numbering is irrelevant in the grand scheme.  Matching between coordinates
topology is the only requirement for proper interpretation of the structure.

> 3) how can I separate, or renumber, the resulting .gro files in order to 
> have a graph in which the fluctuations are not superimposed?

genconf -renumber will renumber your .gro file, but for proper mass-based 
analysis like RMSF, you need a .tpr file, which in this case still contains
chain information.  You can write a simple post-processing script to
the resulting .xvg file.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080



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