clarification needed for wrapAll and wrapWater

From: Yinglong Miao (
Date: Thu Mar 06 2008 - 08:13:40 CST

Dear NAMD developers/users,

In the NVT simulations with periodic boundary conditions (PBC), how does
NAMD treat those atoms outside of the unit cell specified with the
cellBasisvectors in case the lattice is smaller than the structure size? Are
they excluded from the simulation when replicating the unit cell for PBC?
And for the wrapAll and wrapWater options, do they just affect the atomic
coordinates for output or they actually change the atomic configuration for
the simulation at the end of each time step? Can anyone answer these
questions for me? I tried to read the source code to find the answers, but
just got lost in tracking all those variables. I will greatly appreciate
your help.


Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981

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