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<DIV><SPAN class=236585506-13102005><FONT face=Arial color=#0000ff size=2>Thanks
Erik and David. </FONT></SPAN></DIV>
<DIV><SPAN class=236585506-13102005><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=236585506-13102005><FONT face=Arial color=#0000ff size=2>I
compiled with the new toppush.c and reran the simulation. its fine
now. </FONT></SPAN></DIV>
<DIV><SPAN class=236585506-13102005><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=236585506-13102005><FONT face=Arial color=#0000ff
size=2>Regards</FONT></SPAN></DIV>
<DIV><SPAN class=236585506-13102005><FONT face=Arial color=#0000ff
size=2>Sandeep</FONT></SPAN></DIV>
<DIV><SPAN class=236585506-13102005><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=236585506-13102005><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
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<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma size=2>-----Original Message-----<BR><B>From:</B>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <B>On
Behalf Of </B>Erik Lindahl<BR><B>Sent:</B> Thursday, October 13, 2005 6:12
AM<BR><B>To:</B> Discussion list for GROMACS users<BR><B>Subject:</B> Re:
[gmx-users] Discrepancy between Free Energy Perturbation usingGromos96 and
OPLS<BR><BR></FONT></DIV>Hi,
<DIV><BR class=khtml-block-placeholder></DIV>
<DIV><BR>
<DIV>
<DIV>On Oct 12, 2005, at 10:45 PM, David wrote:</DIV><BR
class=Apple-interchange-newline>
<BLOCKQUOTE type="cite">
<DIV style="MARGIN: 0px">On Wed, 2005-10-12 at 22:18 +0200, Erik Lindahl
wrote:</DIV><BR>
<BLOCKQUOTE type="cite">
<DIV style="MARGIN: 0px">Hi,</DIV>
<DIV style="MIN-HEIGHT: 14px; MARGIN: 0px"><BR></DIV>
<DIV style="MARGIN: 0px">A bug indeed. Fixed in both branches of CVS, and
will be in a 3.3.1 <SPAN class=Apple-converted-space></SPAN></DIV>
<DIV style="MARGIN: 0px">update in your near future.</DIV>
<DIV style="MIN-HEIGHT: 14px; MARGIN: 0px"><BR></DIV>
<DIV style="MARGIN: 0px">In the meantime, you can download an updated
src/kernel/toppush.c from</DIV>
<DIV style="MIN-HEIGHT: 14px; MARGIN: 0px"><BR></DIV>
<DIV style="MARGIN: 0px"><A
href="ftp://ftp.gromacs.org/pub/tmp/toppush.c">ftp://ftp.gromacs.org/pub/tmp/toppush.c</A></DIV>
<DIV style="MIN-HEIGHT: 14px; MARGIN: 0px"><BR></DIV><BR></BLOCKQUOTE>
<DIV style="MIN-HEIGHT: 14px; MARGIN: 0px"><BR></DIV>
<DIV style="MARGIN: 0px">It's probably good to note that this is a bug in
grompp rather than</DIV>
<DIV style="MARGIN: 0px">mdrun and that it can be prevented (using manual
labor) by writing the</DIV>
<DIV style="MARGIN: 0px">Ryckaert-Bellemans parameters twice for each
dihedral (such that A and B</DIV>
<DIV style="MARGIN: 0px">state are identical).</DIV></BLOCKQUOTE></DIV><FONT
class=Apple-style-span color=#0000dd><BR
class=khtml-block-placeholder></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#0000dd>Definitely - and you only need
to do it for the handful of dihedrals where the parameters are specified
explicitly in the dihedrals topology section, e.g. with a define
string.</FONT></DIV>
<DIV><FONT class=Apple-style-span color=#0000dd><BR
class=khtml-block-placeholder></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#0000dd>Cheers,</FONT></DIV>
<DIV><FONT class=Apple-style-span color=#0000dd><BR
class=khtml-block-placeholder></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#0000dd>Erik</FONT></DIV>
<DIV><FONT class=Apple-style-span color=#0000dd><BR
class=khtml-block-placeholder></FONT></DIV>
<DIV><FONT class=Apple-style-span color=#0000dd><BR
class=khtml-block-placeholder></FONT></DIV></BLOCKQUOTE></BODY></HTML>