Re: Another question on Diffusion

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Nov 08 2006 - 17:14:08 CST

To elaborate, it *is* possible to unwrap the coordinates later, but it
requires an extra user step.
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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