[gmx-users] regarding micelle and its analysis

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 11 09:05:20 CEST 2012

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.


> how its calculating this value..
> please help me with your answer..
> i am so confused with my analysis..
> thanking you,

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