[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition

Alan alanwilter at gmail.com
Wed Jul 28 08:45:50 CEST 2010

First of all, thanks a lot guys, in special Ilja and Chris.

Indeed, Ilja's observation proved to be corrected, and as Chris suggested,
using the pdb instead of the gro for grompp and the energies matched.

However, I am still uneasy with the fact that pdb2gmx_d and mdrun_d is not
generating a gro with at least 6 decimals instead of the usual 3.

Many thanks,


On Tue, Jul 27, 2010 at 20:34, <gmx-users-request at gromacs.org> wrote:

> Alan: you should try Ilja's suggestion, it was a good one. The idea is
> that during pdb2gmx you may have obtained a .gro file that was rounded
> and then you may have used this .gro as input to grompp and so your
> run did not start with the exact same coordinates in gromacs and namd.
> A similar test would be to be sure that you run grompp with the same
> .pdb file that you used in namd, etc. (or perhaps you already did that?)
> Actually, from what you post below I think that you have your answer.
> Use the orig .pdb into grompp and things should be ok, probably even
> in single precision, although the output .gro will be rounded as you
> see.
> PS: let's keep a positive mood.
> Chris.

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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