[gmx-users] Calculating Eccentricity

[Erik Marklund]

Dear Sanket,

Removing periodicity is difficult if SDS molecules transiently leave the micelle and return after having moved one or more unit cells. You might want to try using gmx clustsize to generate snapshots along the trajectory and use trjconv on them to put all molecules in the same unit cell. Have never used those tools for that purpose so I can’t guarantee that it will work.

Kind regards,
Erik

> On 15 Jun 2016, at 07:28, 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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