Using PBC tools for a cubic and a rectangular box

From: Monika Madhavi (
Date: Tue Mar 27 2018 - 05:34:10 CDT

Dear all,

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
a result.

Thank you.
Best regards,

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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