[gmx-users] how to use g_sham ?

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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