[gmx-users] Questions about g_sham options
David van der Spoel
spoel at xray.bmc.uu.se
Wed Sep 2 17:38:37 CEST 2009
Suman Chakrabarty wrote:
> Hi, I have been trying to use the g_sham tool to generate a
> histogram/free energy profile. Unfortunately a few of the output options
> are not explained in the manual or "g_sham -h". These are -dist, -histo,
> -bin, -map, -ls3, -mdata. Is there any way to know further about them?
Have you looked at the output files? And the default names?
edist -> energy distribution
bindex -> bin index (I guess this meas which structure goes in which bin)
-ls3 -> energy landscape in 3D
Just try it!
> If I need to specify the number of grids in two dimensions (for a free
> energy surface F(X, Y)), may I use, say, -ngrid 100 200? It did not seem
> the -bw (binwidth) option can be changed along different axes, am I right?
> I tried to generate the free energy as a function of intramolecular
> non-bonded interaction energy gathered in the energy.xvg file (two
> column: time and energy). The energy values range from -300 to 0 KJ/mol.
> But when I try the following command: g_sham -f energy.xvg -ls
> gibbs.xpm, 3 files are generated: bindex.ndx, ener.xvg and shamlog.log.
> I am confused with the file ener.xvg since the X-axis ranges from 0 to
> 30! What is contained in this file?
Good question, but you probably need to supply a bit more info to get
> What am I doing wrong? What would be the right way to generate the free
> energy surface for both 1- and 2-dimensional cases? Thanks.
> Suman Chakrabarty.
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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