[gmx-users] regarding micelle and its analysis

[Dallas Warren]

Additionally, you need to be careful with the PBC when using g_gyrate, as if part of the micelle is split across it, then the radius provided will be wrong.

If you have 3 micelles, then you will have to generate an index file with a group for the molecules/atoms within each of the micelles, then pass each group to g_gyrate separately to get the radius for each micelle.

>From what you have written you have calculated the radius of gyration of all of the surfactant molecules within your simulation, which is more than likely not what you want.

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 Mark Abraham
Sent: Wednesday, 11 April 2012 5:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] regarding micelle and its analysis

On 11/04/2012 3:48 PM, priya thiyagarajan wrote:
hello sir,

i am studying about micelle formation of surfactants. i performed my run for 10ns.. when i visualize my final md pdb file i got around 2 to 3 micelles.

my doubt is while performing analysis , g_gyrate giving a value of around 3nm..

this value corresponds to which micelle..

None of them. It corresponds to the group you told g_gyrate to analyse. See g_gyrate -h. Since you haven't told us which group you told g_gyrate to use, you've forced me to guess that you told it to work on all your surfactant molecules. If you'd given a full description of what you'd done, then you'd be more likely to have people wanting and able to help you, and thus be more likely to get useful help. Anyway, g_gyrate can't guess that you want it to look at some magic subsets of the whole system. You have to define the subsets, e.g. with g_select, and only then can g_gyrate compute properties on them.

Mark



how its calculating this value..

please help me with your answer..

i am so confused with my analysis..

thanking you,



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