[gmx-users] PMF Calculations

Arneh Babakhani ababakha at mccammon.ucsd.edu
Thu Jul 27 19:14:35 CEST 2006

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?



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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