[gmx-users] density

Dallas Warren Dallas.Warren at monash.edu
Sun Nov 20 23:34:16 CET 2011

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.warren at 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-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of mohammad agha
Sent: Sunday, 20 November 2011 5:52 PM
To: gmx-users at 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
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