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 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Sunday, 20 November 2011 5:52 PM To: gmx-users@gromacs.org 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
-- 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
