<div class="gmail_quote">On Wed, Sep 2, 2009 at 9:08 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Suman Chakrabarty wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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?<br>
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Have you looked at the output files? And the default names?<br>
edist -> energy distribution<br>
bindex -> bin index (I guess this meas which structure goes in which bin)<br>
-ls3 -> energy landscape in 3D<br>
<br>
Just try it!<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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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?<br>
<br>
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?<br>
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Good question, but you probably need to supply a bit more info to get something interesting...<br></blockquote><div><br><br>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:<br>
<br>Read 1 sets of 3584 points, dt = 1<br><br>There are 32 bins in the 1-dimensional histogram. Beta-Emin = 0<br>Ptot = 3584<br><br>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.<br>
<br>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?<br>
<br>Any suggestion? Thanks.<br><br><br>Regards,<br>Suman.<br><br></div></div><br>