Re: Another question on Diffusion

From: Vinit Rege (vrege_at_asu.edu)
Date: Wed Nov 08 2006 - 19:02:30 CST

OK... I dont think the protein would diffuse laterally so much to to go out
of the box...so I reckon that it would cause no problems...

thanks for your discussions folks... :)

On 11/8/06, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> 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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