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Hi,<br><br>The gro file format, just like the pdb format, is an ancient fixed format.<br>Thus it supports only 3 decimals.<br>Note that this has nothing to do with single or double precision (which have a range<br>of rougly 10^7 and 10^16).<br><br>If pdb2gmx does not mess with your hydrogen and terminal atom coordinates<br>(as some old versions did), you can use pdb2gmx -o conf.pdb for pdb coordinate output<br>or -o conf.g96 for lots of decimals. All Gromacs programs can read pdb and g96<br>instead of gro files.<br><br>Berk<br><br><hr id="stopSpelling">From: alanwilter@gmail.com<br>Date: Wed, 28 Jul 2010 07:45:50 +0100<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition<br><br>First of all, thanks a lot guys, in special Ilja and Chris.<div><br></div><div>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.</div>
<div><br></div><div>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.</div><div><br></div><div>Many thanks,</div><div><br></div><div>
Alan<br><br><div class="ecxgmail_quote">On Tue, Jul 27, 2010 at 20:34, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div id="ecx:1xp" class="ecxii ecxgt">Alan: you should try Ilja's suggestion, it was a good one. The idea is<br>
that during pdb2gmx you may have obtained a .gro file that was rounded<br>
and then you may have used this .gro as input to grompp and so your<br>
run did not start with the exact same coordinates in gromacs and namd.<br>
A similar test would be to be sure that you run grompp with the same<br>
.pdb file that you used in namd, etc. (or perhaps you already did that?)<br>
<br>
Actually, from what you post below I think that you have your answer.<br>
Use the orig .pdb into grompp and things should be ok, probably even<br>
in single precision, although the output .gro will be rounded as you<br>
see.<br>
<br>
PS: let's keep a positive mood.<br>
<br>
Chris.<br></div></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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