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 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] 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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