Thanks Mark and Patrick for your prompt feedback.<br><br>I did look at hydration energies of small molecules and had no problem reproducing the literature data. That being said, i noticed recently that all was not well in some runs. I don't think it is a bug. I am more inclined to think that it is a compilation problem.
<br><br>Let me expand a little bit on the problem i'm experiencing with my binaries.<br><div>The problem is as follows: using g_analyze_d, the average of block averages is not the same as the same as the overall average. Getting a data average should be easy enough, but it is not the case here.
<br></div>
<div> </div>
<div>Here is an example (see Details below):</div>
<div>from 0 to 1000ps ->g_analyze_d average is 1.634425e+03</div>
<div>from 1000 to 2000ps -> g_analyze_d average is 1.634059e+03</div>
<div>from 0 to 2000ps -> g_analyze_d average is 1.637816e+03 ---> a difference of ~ 3kJ/mol compared with the 1ns blocks<br> </div>
<div>from 2000 to 4000 ps > g_analyze_d average is 1.637791e+03 </div>
<div>from 0 to 4000ps -> g_analyze_d average is 1.620341e+03 --> a difference of ~ 17kJ/mol compared with the 2ns blocks<br></div>
<div> </div>
<div>The difference in averages is about 3 kJ/mol for ~ 1million data
points (2 blocks of 1000ps vs 1 block of 2000ps, dt=0.002) and 14-17
kJ/mol for ~2 million data points (2 blocks of 2000ps vs 1 block of
4000ps, dt=0.002
). This is much greater than the double counting of the 1000ps or
2000ps data point would contribute. <br><br></div>
<div>Also, if i process xvg files with some of my own scripts/programs (perl or double-precision fortran), i get:</div>
<div>from 0->4000ps -> average is 1634.2</div>
<div> </div>
<div>Also, if i trim the xvg file (using grep '^\..000') to retain data
points on every other 0.1 ps or so, g_analyze_d gives an average of
1.634125e+03 over the 4000ps run, which looks like the right answer this time.<br><br></div>
<div>This is all very perplexing. <br></div>
<div> </div>Thanks <br>Philippe<br><p>-----Details----</p>
<p>$GROMACS/bin/g_analyze_d -f prod-path.6.coul.l0.5.sol.xvg -e 2000</p>
<p>Read 1 sets of 1000001 points, dt = 0.002</p>
<p> std. dev. relative deviation of<br> standard --------- cumulants from those of<br>set average deviation sqrt(n-1) a Gaussian distribition
<br> cum. 3 cum. 4<br>SS1 1.637816e+03 3.406546e+01 3.406546e-02 -0.168 -0.012</p>
<p><br> $GROMACS/bin/g_analyze_d -f prod-path.6.coul.l0.5.sol.xvg -b 2000 -e 4000</p>
<p>Read 1 sets of 1000001 points, dt = 0.002</p>
<p> std. dev. relative deviation of<br> standard --------- cumulants from those of<br>set average deviation sqrt(n-1) a Gaussian distribition
<br> cum. 3 cum. 4<br>SS1 1.637791e+03 3.383955e+01 3.383955e-02 -0.154 -0.007</p>
<p>$GROMACS/bin/g_analyze_d -f prod-path.6.coul.l0.5.sol.xvg -e 4000<br>Read 1 sets of 2000001 points, dt = 0.002</p>
<p> std. dev. relative deviation of<br> standard --------- cumulants from those of<br>set average deviation sqrt(n-1) a Gaussian distribition
<br> cum. 3 cum. 4<br>SS1 1.620341e+03 3.649526e+01 2.580605e-02 0.676 0.008</p>
<p>---Details end----</p><br><div><span class="gmail_quote">On 6/22/07, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>> wrote:</span><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 a silly problem and would welcome any suggestions. At this point i<br>> suspect that this is a installation or compliation problem.<br>><br>> First, let me say that i am a very unsophiticated user of gromacs.
<br>> Please,<br>> bear with me if there is a well known fix for this.<br>> I have installed gromacs following the instructions on the website<br>> (settings<br>> for double precision and mpi). I started using it and everything seems to
<br>> work pretty well and I have run a number of jobs, mostly FEP's to<br>> familiarize myself better with Gromacs. The results i get are in line<br>> with<br>> published results. However, on some runs, the average dg/dl values i get
<br>> from the outputfile or from using g_analyze_d are out-of-line with what i<br>> can obtain if i process the data myself. For example, i get a very<br>> different average values for 2 block-averages of 1ns each compared to the
<br>> average over the same 2ns. I've tried a few things and it looks like the<br>> problem resides with my gromacs binaries. I can expand on this, if need<br>> be.<br><br>In the absence of a detailed description of what you're doing, it's going
<br>to be hard to convince anyone that the problem resides with GROMACS rather<br>than your use of it, or your other method you refer to - particularly as<br>an inexperienced user. I'd suggest developing scripts that do an entire
<br>calculation so that you have some basis for recording exactly what you did<br>and making it reproducible.<br><br>> Before I try reinstalling gromacs, i would appreciate getting some<br>> feedback<br>> on the key settings for a porper gromacs installation and how to check for
<br>> potential problems.<br>> Also, is there a set of test-jobs i can run to convince myself that i<br>> installed gromacs properly and that everything is working properly?<br><br>The installation guide on the website is fine for the vast majority of
<br>systems. I'm not aware of a test suite per se, because MD is not<br>reproducible between slightly different hardware. You should be able to<br>reproduce ensemble averages with accuracy, however.<br><br>Mark<br><br>
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