Thanks Prof. Warren
________________________________
From: Dallas Warren <dallas.war...@monash.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Tuesday, November 22, 2011 12:23 AM
Subject: RE: [gmx-users] density
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.war...@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...@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.war...@monash.edu>
To: mohammad agha <mra...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@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.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
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