I don’t do COM calculations, so don’t know directly, but have a read of “g_rdf –h”, method is outlined there and I suspect there are a number of discussions on it within the emailing list archive that you should search.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: mohammad agha [mailto:[email protected]] Sent: Tuesday, 22 November 2011 4:28 AM To: Dallas Warren Subject: Re: [gmx-users] density Dear Prof. Warren Excuse me, may I know that how to obtain the average radial density functions relative to the center of mass with g_rdf? I think these plots are produced by counting the number of selected atoms that are within the x angstrom wide shells around the micelle COM, and I think that I should use from : N= 4 π ρ∫ 0 00 r2 g(r) dr. , but I don't know how to find N and what is the computation carefully? Please help me. Best Regards Sara ________________________________ From: Dallas Warren <[email protected]<mailto:[email protected]>> To: mohammad agha <[email protected]<mailto:[email protected]>>; Discussion list for GROMACS users <[email protected]<mailto:[email protected]>> Sent: Monday, November 21, 2011 2:04 AM Subject: RE: [gmx-users] density Last bit here, that is probably done using a RDF, which is a probability function, which you can then convert into a number of atoms in each shell. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected]<mailto:[email protected]> +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected]<mailto:[email protected]> [mailto:[email protected]] On Behalf Of mohammad agha Sent: Sunday, 20 November 2011 5:52 PM To: [email protected]<mailto:[email protected]> Subject: [gmx-users] density Dear Prof. I have problems about density. I equilibrated my system consist 500 surfactants and 60000 water molecules in martini coarse-grained for 120 ns and my results of g_energy next pr.mdp for density are: average = 907.701 err.est = 0.61 rmsd = 2.54989 tot-drift = -3.4173 I don't know about good quantity of err.est, rmsd and tot-drift for density adjustment? and when my system has been equilibrated? May I know about my problem, please? On the other hand, "density distribution for different groups of the system in terms of their distance from micell's COM distance" is considered In the articles about surfactants. I think that it is possible with g_density but this program compute the density as the function of box(nm). May I know about this problem, Please? Best Regards sara
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