<div dir="ltr">Thanks for your answers,<br><br>I tried to struggle a bit more with that today.<br>my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and pullx-files.dat) are fine and consistent with other in terms of file numbering. <br>
<br>i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler.<br><br>i run: <b>g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 1000 </b>(my data is 16ns long and i ignore the first ns)<br><br>and it starts reporting that the file are read:<br>
<br>Reading file topol742.tpr, VERSION 4.0.5 (single precision)<br>File topol742.tpr, 1 groups, geometry "distance", dimensions [N Y N], (1 dimensions)<br> grp 0) k = 1000.000 inittial distance = 2.41331<br>
Reading file topol748.tpr, VERSION 4.0.5 (single precision)<br>Reading file topol761.tpr, VERSION 4.0.5 (single precision)<br>Reading file topol792.tpr, VERSION 4.0.5 (single precision)<br>and so on..<br><br>it reports that the boundaries are found and continue to read until it stucks..<br>
<br>However, when i do the WHAM with the pullx files (i.e., -ix pullx-files instead of -if pullf-files.dat) the wham converges within a reasonable time to a PMF profile which not so smooth.<br><br>i therefore have some questions:<br>
1) what is the difference in the profiles for using pullx or pullf files?<br>2) suppose that my histograms overlap is poor for some locations along the pulling vector, how one can solve that? <br>3) To generate the input configurations - what is the ideal pulling procedure? ( i used pull = constant_force, with a small value of K1)<br>
<br>Again, Thanks a lot for the quick reply<br>Amir<br> <br><div class="gmail_quote">On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub <span dir="ltr"><<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Amir Marcovitz wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi All,<br>
<br>
I have some problems with g_wham, and i already gone through all the postings and didn't find a hint..<br>
<br>
basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all steps, i.e., minimization, equilibration etc. up to that point work fine)<br>
from the pulling i generated input configurations for the umbrella sampling runs (pull=umbrella , rate=0.0), which are 15 ns long<br>
and collected all the output pullf.xvg and *.tpr files.<br>
</blockquote></div>
You could also run g_wham -histonly to get the histogram file. Then check with xmgrace -nxy histo.xvg whether the histograms properly overlap.<br>
<br>
But if they do not overlap, I would rather expect g_wham to give a zero PMF or to iterate forever, so not sure what is wrong.<br>
<br>
Jochen<div><br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
i then run g_wham (with -it and -if) and it works fine at the beginning, but then the computer simply gets stuck (!?) and the calculation is killed - with no error massage.<br>
<br>
what is it that I'm doing wrong?<br>
it looks like my output data (pullf and tpr files) are fine, but is it possible that some of them causing the problem?<br>
<br>
this is really frustrating..<br>
need your help,<br>
Amir<br>
<br>
</blockquote>
<br>
<br></div><font color="#888888">
-- <br>
---------------------------------------------------<br>
Dr. Jochen Hub<br>
Molecular Biophysics group<br>
Dept. of Cell & Molecular Biology<br>
Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>
Phone: +46-18-4714451 Fax: +46-18-511755<br>
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