On Wed, Sep 2, 2009 at 9:08 PM, David van der Spoel <[email protected]>wrote:
> 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 > something interesting... > My energy.xvg file contains the output from g_energy where first column is time and second column is LJ short range interaction energy (LJ-SR:Protein Protein). The values of energy are distributed between -300 to 0 KJ/mol. So I expect a histogram or free energy as a function of this energy, where X-axis values would range from -300 to 0 KJ/mol. But when I try the above command, or simply "g_sham -f energy.xvg" the screen output says: Read 1 sets of 3584 points, dt = 1 There are 32 bins in the 1-dimensional histogram. Beta-Emin = 0 Ptot = 3584 The output file ener.xvg looks like a free energy surface (1D), but the X-axis values range from 0 to 30, instead of -300 to 0. I am not sure whether ener.xvg is supposed to contain the free energy or not. But even if I try with "-ls gibbs.xpm" option, no gibbs.xpm file comes as output. Probably that is only relevant for 2D free enegry surfaces? Any suggestion? Thanks. Regards, Suman.
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