**From:** Monika Madhavi (*monikamadhavi_at_gmail.com*)

**Date:** Tue Mar 27 2018 - 05:34:10 CDT

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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

and

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,

Monika

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

**Next message:**Brian Radak: "Re: Using PBC tools for a cubic and a rectangular box"**Previous message:**Vermaas, Joshua: "Re: NAMD Simulation in a laptop"**Next in thread:**Brian Radak: "Re: Using PBC tools for a cubic and a rectangular box"**Reply:**Brian Radak: "Re: Using PBC tools for a cubic and a rectangular box"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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