On 10/2/10 Oct 2,10:51 PM, Петр Попов wrote:
Hello, dears gmx-users!
I posted a message, but didn't get a response, it was my first one, so
may be I did something wrong. Anyway, here it is:
I've already run md and got pmf and it's correct. But I want to get
not just a pmf of total force, but several profiles each of which
corresponds to the different components. For example, one pmf -
protein-protein interactions, another - protein-solvent interactions.
Or another, one pmf corresponds to electrostatic, another to VdW etc.
Should I change a program's code? If so, tell me please in what
exactly program?
Or may be gromacs have similar functions? Or is the another way to
split pmf?
Hi, what we did some years ago (Hub and de Groot, Does CO2 permeate
through aquaporin-1, Biophys J 91, 842-848 (2006)), we used the energy
file to decompose the potential (that is the enthalpic contribution to
the PMF) into solute-water, solute-protein interactions, etc. You would
have to make a tpr file with different energy groups and then do a
rerun. Note that we do not decompose the mean force with that procedure
though.
I hope this helps.
Cheers,
Jochen
Thank you for your attention!
--
---------------------------------------------------
Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell& Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
http://xray.bmc.uu.se/~jochen/index.html
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