[gmx-users] PMF Calculations

[David van der Spoel]

Arneh Babakhani wrote:
> Thanks.  In GMX, is there a tool for integrating the mean force from an 
> ensemble of configurations (in order to obtain the pmf)? Or does one 
> have to do that by other means?
> 
g_analyze -integrate

> Thanks,
> 
> Arneh
> 
> David van der Spoel wrote:
>> Arneh Babakhani wrote:
>>> Hello,
>>>
>>> Can someone please describe the general procedure for PMF (potential 
>>> of mean force) calculations using GROMACS? Is there an analysis tool 
>>> for this (I didn't see one), or a combination of tools?  (Please 
>>> note: I'm not asking for details.  I'm just seeking a general method 
>>> for calculating PMF. I can work out the details, I'm just not sure 
>>> where to begin!).
>>>
>> maybe you want to check the section about AFM pulling in the manual.
>>
>>
>>> Thank you kindly,
>>>
>>> Arneh
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>>
>>
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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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