[gmx-users] Calculating Eccentricity

[Tsjerk Wassenaar]

Hi Sanket,

You probably want the clustering routine of trjconv. And then calculate the
principal axes of the micelle. The instantaneous value does not mean much,
but a an average non-zero eccentricity would suggest with a greater extent
than without peptide would suggest an effect. Note that you do need the
control experiment, because the eccentricity cannot have a mean value of
zero in a dynamic system.

Cheers,

Tsjerk


On Wed, Jun 15, 2016 at 8:28 AM, Sanket Ghawali <sanket.ghawali at gmail.com>
wrote:

> Dear gmx user
>
> I am performing a MD simulation of peptides in sds for 100ns. After the
> completion of my production I am unable to remove the periodic boundary
> condition.
> I wanted to Calculate the eccentricity of the SDS micelle after 100ns, does
> the periodic boundary condition affect my eccentricity result ?
> Is it necessary first to remove the pbc effect and then calculate
> Eccentricity.
> Also does the high eccentricity value obtained after 100ns tell me that the
> micelle is distorted and the peptide has some activity?
>
> Thank you.
> Sanket
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-- 
Tsjerk A. Wassenaar, Ph.D.