[gmx-users] PMF Calculations
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jul 28 08:38:11 CEST 2006
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?
> David van der Spoel wrote:
>> Arneh Babakhani wrote:
>>> 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,
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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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