rescaling of coordinates in PBC simulations

From: Giovanni Bellesia (
Date: Thu Aug 11 2005 - 12:41:52 CDT

Hi all,
I ran an MD simulation (under PBC and at constant temperature) on a
system consisting of 20 short peptides (strands)
assembled unidimensionally in a helical beta-tape.
Now, I should calculate some structural parameters like interstrand
hydrogen-bonds, interstrand distance, twist angle etc ... which all involve
calculations based on reciprocal positions of strands.

Visual analysis of the trajectory shows that about 1/3 of the short
peptides (1/3 of the supramolecular tape) is out
of the central box during the most part of my sim.

Is there any easy way for rescaling the coordinates, putting back in the
central box all the molecules and getting right
structural results ?



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