[gmx-users] X and Y dimensions in nanometers

[Mark Abraham]

On 9/09/2011 4:12 AM, Conrado Pedebos wrote:
> Dear gmx-users,
>
> I am working with a system composed by 20 molecules which are 
> aggregated in water. I want to calculate the dimensions of this 
> aggregate, but it has an elipsoidal shape, instead of a globular 
> shape, as follows in this representation:
>
>                    |
>          _____|______
> -----( ____________)------X
>                    |
>                    |
>                   Y
>
> Which gromacs tool could I use to perform this analysis and calculate 
> X and Y (nm) as a function of time?
>

I don't think there is anything to do X, but g_mindist -max can do Y. 
Aligning your principal axes with the coordinate axes and looking at the 
distribution of the coordinates found with g_traj and then g_analyze is 
probably the best you can do.

Mark
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