[gmx-users] how to use g_sham ?
David van der Spoel
spoel at xray.bmc.uu.se
Sat May 20 15:37:23 CEST 2006
>> Liang wrote:
>>> Dear all users :
>>> g_sham is a new program in 3.3 and i cant find any discussion about
>>> how to use in mailing lists, and i didnt catch the point about the
>>> instructions in user manual.
>>> Is it possible to draw pics about PMF or free energy landscape using
>>> some special coordinates, like RMSD, potential, or dihedral angle
>>> variations etc. ?
>> all yes.
>> have you run g_sham -h ?
> YES, g_sham -h is the same as user manual, but i still have some puzzle.
> for example, i wanna calculate the RMSD vary with potential energy, so i
> generate rmsd.xvg and energy.xvg.
> g_sham -f rmsd.xvg -ene energy.xvg
> is it right?
> and how to set up the parameter of free energy landscape vectors?
> like -dim -ngrid -xmin -xmax -gmax
> THANKS SO MUCH !!
just try things out.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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