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On 18/04/2012 10:32 PM, Tom Kirchner wrote:
<blockquote cite="mid:4F8EB456.8050100@mis.mpg.de" type="cite">
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charset=ISO-8859-1">
Of my first mail, only the attachment was printed in the mailing
list. I am sorry for the inconvenience. The attachment can be sent
by request.<br>
</blockquote>
<br>
They came through.<br>
<br>
<blockquote cite="mid:4F8EB456.8050100@mis.mpg.de" type="cite"> <br>
----------<br>
<br>
Hi all,<br>
<br>
Recently, I posted a problem concerning the usage of polarizable
ff in conjunction with free energy calculation. Sadly I got no
answer, but after some research, I hope I have isolated the
problem.<br>
</blockquote>
<br>
Thanks for the clear report.<br>
<br>
<blockquote cite="mid:4F8EB456.8050100@mis.mpg.de" type="cite"> <br>
Using a polarizable ff without free energy makes no problems. As
soon as free energy is turned on, Gromacs gives the error:<br>
<br>
<i>Program mdrun_d, VERSION 4.5.5<br>
Source code file: [...]/src/gromacs-4.5.5/src/mdlib/shellfc.c,
line: 365<br>
<br>
Fatal error:<br>
polarize can not be used with qA != qB</i><br>
<br>
This error occurs, even if the atom and the shell particle have
the same charge or are unaltered by the free energy option, e.g.
lambda=0.0 and multiplication with (1-lambda). Because of this, I
guess there is a problem with different charge variables being
single and double precision due to multiplication with lambda.<br>
</blockquote>
<br>
... well, likely some kind of floating-point-algebra failure,
anyway.<br>
<br>
<blockquote cite="mid:4F8EB456.8050100@mis.mpg.de" type="cite"> <br>
The error occurs in this segment of shellfc.c:<br>
<small><big><br>
case F_POLARIZATION:<br>
if (qS != atom[aS].qB)<br>
gmx_fatal(FARGS,"polarize can not be used with qA !=
qB");</big><br>
</small><br>
If anybody knows, how to correct this, I would be very grateful.<br>
</blockquote>
<br>
I've uploaded a draft fix to <a class="moz-txt-link-freetext" href="https://gerrit.gromacs.org/#/c/746/">https://gerrit.gromacs.org/#/c/746/</a><br>
<br>
<blockquote cite="mid:4F8EB456.8050100@mis.mpg.de" type="cite">
Moreover I'm wondering about the physical meaning of the
if-statement. <br>
</blockquote>
<br>
No idea.<br>
<br>
Mark<br>
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