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.
-Justin
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v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, which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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--
========================================
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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