Re: Changing Boundary conditions from PBC to non-periodic

From: Gianluca Interlandi (
Date: Thu Nov 19 2015 - 14:30:16 CST

You should look at the pbctool plugin:

You should use the option "wrap" to wrap the water molecules around the


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
                     +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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