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On 9/18/10 Sep 18,10:17 PM, Jochen Hub wrote:
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On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote:
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cite="mid:AANLkTimdV65iBs8wTVFfKVcSvKg8K5M=p3myAUZZfBDf@mail.gmail.com"
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Hi gmx-users
<div>I finished a series of pulling runs using the
"periodic_direction" option </div>
<div>and when I run the g_wham analysis I received the following
message.</div>
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<div> <br>
</div>
<div>
<div>-------------------------------------------------------</div>
<div>Program g_wham, VERSION 4.5</div>
<div>Source code file: gmx_wham.c, line: 1369</div>
<div><br>
</div>
<div>Fatal error:</div>
<div>Pull geometry direction_periodic not supported</div>
<div><br>
</div>
<div>For more information and tips for troubleshooting, please
check the GROMACS</div>
<div>website at <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div>
<div>-------------------------------------------------------</div>
<div><br>
</div>
Is there any way to circumvent this or should I redo all my
simulations with the </div>
<div>option of "direction" instead "direction_periodic"?</div>
</blockquote>
Hi Eudes,<br>
<br>
the g_wham has not been properly updated to gmx 4.5 yet. I'll do
that as soon as possible. For now, I would recommend to use g_traj
to write the coordinates of your pull group and your reference
group and to write a script that writes pdo files. Check g_wham -h
to see a typical pdo header. Then use g_wham -ip to compute your
PMFs.<br>
<br>
<br>
</blockquote>
<br>
Hi Eudes,<br>
<br>
the latest g_wham is now in (at least in the git version of) gromacs
4.5x. For your geometry, you'll have to write the pull forces
(pullf.xvg files) and read those into g_wham with -if. g_wham cannot
read the pullx files written by geometry "direction_periodic" or
"direction".<br>
<br>
Please let me know it if g_wham makes any more trouble.<br>
<br>
Cheers,<br>
<br>
Jochen<br>
<br>
<br>
<br>
<pre class="moz-signature" cols="72">--
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Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
<a class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/~jochen/index.html">http://xray.bmc.uu.se/~jochen/index.html</a>
---------------------------------------------------
</pre>
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