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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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