[gmx-users] Questions about g_sham

Warren Gallin wgallin at ualberta.ca
Wed Jun 23 19:17:49 CEST 2010

Hi all,

	I am trying to use g_sham to generate a free-energy profile based on the end-to-end distances of a peptide.

	The only documentation that I have been able to find is in the GROMACS v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, which I assume is the most current.

	My input file (dist_div.xvg) is a simple list of distances, one per line, stripped out of the g_dist output from a trajectory.

The command line is:

g_sham -f dist_div.xvg -notime -ls Free.xpm -dist energy_dist.xvg -histo histogram.xvg -xvgr

The program runs without errors or warnings, but:
1) There is no Free.xpm or histogram.xvg file written
2) The file energy_dist.xvg does not have any of the expected legend code, it is only the data for bin number vs. Energy
3) The bin sizes do not seem to be correct i.e. when I divide the difference between the largest number and the smallest number by 32, and then check the expected boundary values for bin 0 and bin 31, I find lengths in the wrong bins

	Can anyone give me some insight into the actual workings of g_sham and what I might be doing wrong (or incorrectly expecting) here?

Warren Gallin


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