2010/10/4 Jochen Hub <joc...@xray.bmc.uu.se>
> 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<http://xray.bmc.uu.se/%7Ejochen/index.html> > --------------------------------------------------- > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > Thank you for your response and for the article! I think it is what I want. But could you explain it more detailed? I mean, how did you decompose the potential?
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