[gmx-users] Questions about g_sham
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 23 20:03:58 CEST 2010
Warren Gallin wrote:
> 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?
Sounds to me like a problem for PMF, but I seem to recall you had some issues
with that. g_sham requires 2 dimensions, so you can't use it for your purposes.
> 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 The only documentation that I have been able to find is in the GROMACS v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, which I assume is the most current.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.
>>> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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