<div dir="ltr"><div>Thank you Jochem,</div>
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<div>In your last reply, did you mean that i can perform the WHAM on Various histograms that were collected with different force constants? i mean , will it know to do the correction for the biasing potential<br></div>
<div>amir<br></div>
<div class="gmail_quote">On Fri, Apr 30, 2010 at 4:00 PM, Jochen Hub <span dir="ltr"><<a href="mailto:jochen@xray.bmc.uu.se">jochen@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br><br>Amir Marcovitz wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">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>
i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler.<br></blockquote><br>Time and time again, we have to point out the bold warning on the Downloads page:<br><br>"WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc."<br>
<br>Buggy behavior that is difficult to diagnose is often due to these faulty compilers.<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>i run: *g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 1000 *(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></blockquote><br>In principle, there probably shouldn't be any, but if there is perhaps someone else has seen that.<br></blockquote></div>It should not make any difference at all. It it does, there is something wrong with the data or g_wham is buggy. With the pullf files, g_wham simply computes the pullx values from the force and the force constant. This is not really required since it is more natural to just work with the pullx, but I added to for the case that someone forgot to write the pullx and only has the pullf files.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">2) suppose that my histograms overlap is poor for some locations along the pulling vector, how one can solve that?<br>
</blockquote><br>Better sampling (more time) within the sampling windows, or more closely-spaced windows.<br></blockquote></div>And maybe stronger force constants. g_wham can combine the runs with smaller and larger force constants, that is no problem.<br>
<br>That is probably the reason for the weired PMF!<br><font color="#888888"><br>Jochen</font>
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<div class="h5"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">3) To generate the input configurations - what is the ideal pulling procedure? ( i used pull = constant_force, with a small value of K1)<br>
</blockquote><br>There isn't one "best" method, per se. The only criterion is that you have generated configurations from which you can derive reasonably-spaced windows in which you do sufficient sampling.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Again, Thanks a lot for the quick reply<br>Amir<br><br>On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub <<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</a> <mailto:<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</a>>> wrote:<br>
<br> Amir Marcovitz wrote:<br><br> Hi All,<br><br> I have some problems with g_wham, and i already gone through all<br> the postings and didn't find a hint..<br><br> basically, I'm trying to calculate PMF between two charged<br>
plates. I've performed a pulling simulation between the 2 plates<br> according to Justin's UMBRELLA tutorial in the website (all<br> steps, i.e., minimization, equilibration etc. up to that point<br>
work fine)<br> from the pulling i generated input configurations for the<br> umbrella sampling runs (pull=umbrella , rate=0.0), which are 15<br> ns long<br> and collected all the output pullf.xvg and *.tpr files.<br>
<br> You could also run g_wham -histonly to get the histogram file. Then<br> check with xmgrace -nxy histo.xvg whether the histograms properly<br> overlap.<br><br> But if they do not overlap, I would rather expect g_wham to give a<br>
zero PMF or to iterate forever, so not sure what is wrong.<br><br> Jochen<br><br><br><br><br> i then run g_wham (with -it and -if) and it works fine at the<br> beginning, but then the computer simply gets stuck (!?) and the<br>
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<br> is it possible that some of them causing the problem?<br>
<br> this is really frustrating..<br> need your help,<br> Amir<br><br><br><br> -- ---------------------------------------------------<br> Dr. Jochen Hub<br> Molecular Biophysics group<br> Dept. of Cell & Molecular Biology<br>
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