[gmx-users] how to use g_sham ?
petrucci86 at vip.sina.com
Sat May 20 15:10:21 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 !!
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