[gmx-users] Questions about g_sham

[Warren Gallin]

OK, what if I have only one dimension (end-to-end distance), is there any way to do that in GROMACS, or is the best way to just write a little app for myself?

Warren Gallin

On 2010-06-23, at 11:29 AM, Justin A. Lemkul wrote:

> 
> 
> 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 	The only documentation that I have been able to find is in the GROMACS v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, which I assume is the most current.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 preference.
> 
> -Justin
> 
>> Warren Gallin
>> 	
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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