[gmx-users] Installation/compilation problem ---v3.3.1

David van der Spoel spoel at xray.bmc.uu.se
Sat Jun 23 22:34:21 CEST 2007

philippe ayala wrote:
> Thanks Mark and Patrick for your prompt feedback.
> 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.
> Let me expand a  little bit on the problem i'm experiencing with my 
> binaries.
> 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.
> Here is an example (see Details below):
> from 0 to 1000ps ->g_analyze_d average is 1.634425e+03
> from 1000 to 2000ps -> g_analyze_d average is 1.634059e+03
> from 0 to 2000ps -> g_analyze_d average is 1.637816e+03   ---> a 
> difference of ~ 3kJ/mol compared with the 1ns blocks
> from 2000 to 4000 ps > g_analyze_d average is 1.637791e+03  
> from 0 to 4000ps -> g_analyze_d average is 1.620341e+03  --> a 
> difference of ~ 17kJ/mol compared with the 2ns blocks
> 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.  
> Also, if i process xvg files with some of my own scripts/programs (perl 
> or double-precision fortran), i get:
> from 0->4000ps -> average is  1634.2
> 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.
> This is all very perplexing.
> Thanks
> Philippe
First gromacs uses more frames than you have saved the energy in to 
compute averages and fluctuations. This is described in an appendix of 
the manual. The code is quite complicated. Maybe you should report a 
bugzilla so that we can verify it.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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