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

Justin A. Lemkul jalemkul at vt.edu
Fri May 13 14:46:00 CEST 2011

Anna Marabotti wrote:
> 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).

There were extensive changes to many programs (not just pdb2gmx) that were 
connected with the new numbering scheme.  It doesn't surprise me at all that 
4.5.4 does this, but I'm unable to give you an exact reason.



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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