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="gmail_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="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div id=":1xp" class="ii gt">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/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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