[gmx-users] analysis of PMF calculations

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 11 22:33:54 CEST 2011

Rebeca García Fandiño wrote:
> Hi,
> thanks a lot for your quick answer...
> However, when I try the options you suggest for -cycl/nocycl, the 
> program indeed ask for arguments:
> -------------------------------------------------------
> Program g_wham, VERSION 4.5
> Source code file: statutil.c, line: 338
> Fatal error:
> Expected a string argument for option -cycl
> -----------------------------------------------------------------

Upgrade to version 4.5.4 and try again.  There have been improvements to g_wham.

> Besides, I think you have misunderstood me. When I use the option -cycl 
> YES it's when I obtain the second column with zeros. I am working with a 

Based on what your message said, I thought I understood perfectly.  Quoting:

When I use:

/GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max 
2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip ./pdo-files.dat -cycl yes

I get a curve with no errors, however if I don't use the option "-cycl yes"

Here everything sounds like it worked as expected and then you report the error, 
quoting again:

/GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max 
2.4750 -o pmf_1_no_cycl.xvg -hist histogram_no_cycl.xvg -ip ./pdo-files.dat

I get a profile where the second column is all "zero"

Nevertheless, you should still use version 4.5.4 g_wham and report back if you 
have problems.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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