From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Nov 19 2015 - 14:30:16 CST
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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