waterbox changes shape during steered molecular dynamics

From: Mert Gür (gurmert_at_gmail.com)
Date: Mon Jun 21 2010 - 14:50:58 CDT

Dear all,
I am trying to do steered molecular dynamics starting from random
structures in the trajectory.For that reason I am loading the
trajectory to VMD and then simply save the selected frames as pdb
files.I am using them as initial structures for SMD. Since I cant use
restart files anymore, I am setting the temperature
and the cellBasisvector at the beginning (as shown bellow. I have only
shown the some part of my conf file).The waterbox changes its shape
significantly during the simulation.I observed such an behavior only
ones when I had forgotten to set the periodic boundary conditions and
the water approached its minimum energy shape which is a sphere.
Does this make sense to anyone?

structure ../common/ionized.psf
coordinates smdref550.pdb
set temperature 310

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