Re: Another question on Diffusion

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Nov 08 2006 - 17:12:23 CST

Actually, you really should have wrapall off if you want to calculate
diffusion coefficients. Otherwise, the wrapping will set an upper limit
to how far anything can move. This isn't always an issue if you use a
subset of a bilayer over relatively short timescales, but you're better
off not wrapping anything. Note that wrapping only affects the
appearance of the coordinates; the actual calculations are the same
either way.
Peter

Neelanjana Sengupta wrote:
> Since your system is in a bilayer, it should be fine. Had it been in a
> solvent like water, you could have considered not doing wrapAll.
>
> On 11/8/06, *Vinit Rege * <vrege_at_asu.edu <mailto:vrege_at_asu.edu>> wrote:
>
> I was reading some of the posts here and I am not confused a bit
> about using WrapAll in the simulations. I am running MD on a
> system of bacteriorhodopsin in POPC bilayer with PBC and wrapall
> set ON... I am trying to get RMSD plot and eventually Diffusion
> coefficients... Am I being wrong to use WrapAll ?
>
> sincerely,
> Vinit
>
>
>
>
> --
> ****************************************
> Neelanjana Sengupta, PhD student
> Dept. of Chemistry
> Univ. of California-Irvine
> Irvine, CA 92697
> USA
> Phone: 1-949-824 9921
> email: sengupta_at_uci.edu <mailto:sengupta_at_uci.edu>
> ****************************************

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