[gmx-users] density

[Dallas Warren]

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
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: mohammad agha [mailto:mra_bu at yahoo.com]
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 <Dallas.Warren at monash.edu<mailto:Dallas.Warren at monash.edu>>
To: mohammad agha <mra_bu at yahoo.com<mailto:mra_bu at yahoo.com>>; Discussion list for GROMACS users <gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>
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
dallas.warren at monash.edu<mailto: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> [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<mailto: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
sara

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