Changing Boundary conditions from PBC to non-periodic

From: Mahdi Tavakol (
Date: Thu Nov 19 2015 - 12:30:23 CST

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 advanceMahdi Tavakol

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