Re: Using PBC tools for a cubic and a rectangular box

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Mar 27 2018 - 08:09:43 CDT

Hi Monika,

The usage of pbctools is a little more complicated than what you are doing.
I recommend looking at the plugin documentation (
https://www-s.ks.uiuc.edu/Research/vmd/plugins/pbctools/)

Short explanation - pbctools does not know anything about your box
dimensions (which MUST be orthorhombic) until you tell it. That information
is NOT extracted from the DCD frames, but can be read from an XST
trajectory.

This will assign your fixed box size to all frames, *then* you can unwrap.
% pbc set cell {30.0 30.0 30.0} -all

HTH,
BKR

On Tue, Mar 27, 2018 at 6:34 AM, Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> 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.
>

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