[gmx-users] Questions about g_sham

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 23 19:29:40 CEST 2010

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 	The only documentation that I have been able to find is in the GROMACS v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, which I assume is the most current.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

Your input file is incorrect.  In order to generate a 2-D free energy surface, 
you need to feed g_sham two variables.  The format of the input .xvg file needs 
to be one of two options:

1. with time

	time	value1	value2

2. without time
	value1	value2

The difference can be interpreted by g_sham -[no]time, depending on your 


> Warren Gallin


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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