AW: Changing Boundary conditions from PBC to non-periodic

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Nov 20 2015 - 01:52:26 CST

How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. What are you trying to accomplish?

Norman Geist

> -----Urspr√ľngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Gianluca Interlandi
> Gesendet: Donnerstag, 19. November 2015 21:30
> An: NAMD List <namd-l_at_ks.uiuc.edu>; Mahdi Tavakol
> <mahditavakol_at_ymail.com>
> Betreff: Re: namd-l: Changing Boundary conditions from PBC to non-periodic
>
> You should look at the pbctool plugin:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>
> You should use the option "wrap" to wrap the water molecules around the
> protein.
>
> Gianluca
>
> On Thu, 19 Nov 2015, Mahdi Tavakol wrote:
>
> > Dear NAMD users,
> >
> > A portion of my protein is outside of the simulation box. But, using the PBC
> my
> > protein is continuous. I empolyed PBC condition with wraping water and
> wraping all
> > options on.
> > Now, I want to use the *.restart.coor and *.restart.vel from the
> equilibration to
> > start another simulation with non-periodic boundary condition. Warping
> .restart.coor
> > file with the values of PBC size obtained form the last value of .xsc file was
> not
> > successful, as my system became unstable.
> >
> > What should I do?
> >
> >
> > Any help is appreciated in advance
> > Mahdi Tavakol
> >
> >
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

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