From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Tue Mar 27 2018 - 05:34:10 CDT
I did a water simulation in a cubic box (30x30x30) Å and in a rectangular
box (60x60x120) and I calculated the same property of water (spin
relaxation rate constants). However, the two results I get are different to
each other. I suspect this could be a problem with PBC.
In each simulation, I used cellBasisVectors as the length of each side of
the box. i.e.
30 0 0
0 30 0
0 0 30
60 0 0
0 60 0
0 0 120
and when analyzing the trajectory using a tcl script in vmd, I used the
following command to unwrap the system
package require pbctools
pbc unwrap -molid $mol -all
But the result is the same as before.
I am not very confident about how pbc works in namd and how to unwrap the
trajectory properly. I would like to know whether the way I unwrapped the
trajectory is correct and some insight for the reasons to get this kind of
-- W.A.Monika Madhavi Lecturer (Probation), Department of Physics, University of Colombo.
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