[gmx-users] how to use g_sham ?

Liang 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


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