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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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
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