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

Berk Hess gmx3 at hotmail.com
Wed Jul 28 11:59:32 CEST 2010


The gro file format, just like the pdb format, is an ancient fixed format.
Thus it supports only 3 decimals.
Note that this has nothing to do with single or double precision (which have a range
of rougly 10^7 and 10^16).

If pdb2gmx does not mess with your hydrogen and terminal atom coordinates
(as some old versions did), you can use pdb2gmx -o conf.pdb for pdb coordinate output
or -o conf.g96 for lots of decimals. All Gromacs programs can read pdb and g96
instead of gro files.


From: alanwilter at gmail.com
Date: Wed, 28 Jul 2010 07:45:50 +0100
To: gmx-users at gromacs.org
Subject: [gmx-users] Re: gromacs energies very different from other MD	engine for the very same system and condition

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


PS: let's keep a positive mood.


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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