Are coordinates in the tclForces module loaded as wrapped?

From: Salvatore Mario Cosseddu (
Date: Tue Apr 16 2013 - 05:12:08 CDT

Dear All,

My question is quite simple: when loadcoords is used within the
calcforces proc, the coords are wrapped or unwrapped?

I'm asking it, since I'm experiencing a very strange behavior. I created
a force script to apply a spherical harmonic on a subset of ion in my
system (ion) from the the COM of a region of my protein (I'm attaching
the simplified version, containing the core of the script). It has kept
failing, in the sense that it work properly the first half of the
simulation, but it starts failing with the ions that, during the
simulation, crossed the boundaries. That would be understandable if the
coordinates are not wrapped when loaded via loadcoords. Before
implementing the periodic boundary condition in a naive way (I'm
simulating in the NpT, but I can not access to the actual box sizes from
within the proc), I'd like to know your opinion, if that can be the
origin of the error.

Thanks and best regards

Salvatore Cosseddu
PhD student
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom

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