Liang wrote:
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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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