From: Zumot, Elia Nabil (enz1_at_pitt.edu)
Date: Fri Apr 22 2011 - 22:52:11 CDT
Thank you for responding Axel but bear with me please,
> and rightfully so, as this does not make sense and is
> in violation of the documentation.
Does this mean that once a molecule has left the boundaries there is no way in VMD to restore it to within the original/central box (rewrite its coordinates as if it had been wrapped)?
> if you want to wrap around {132 96 110} you should use
> that as argument to -center.
> also, please note, that tcl lists/vectors have no comma.
I want the center of the box to be 0 0 0, and the x, y and z dimensions to be 132, 96 and 110.
This one doesn't work either:
% pbc wrap -orthorhombic {132 96 110} -center {0 0 0} -sel "all"
error: pbcwrap: unknown option: 132 96 110
Thanks again
Elia
Elia Zomot, PhD
Computational and Systems Biology Department
School of Medicine, University of Pittsburgh
3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
Voice: 412 648 7785 - Fax: 412 648 3163
enz1_at_pitt.edu
________________________________________
From: Axel Kohlmeyer [akohlmey_at_gmail.com]
Sent: Friday, April 22, 2011 11:21 PM
To: Zumot, Elia Nabil
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: pbc wrap option for x,y,z lengths
On Fri, Apr 22, 2011 at 3:03 PM, Zumot, Elia Nabil <enz1_at_pitt.edu> wrote:
> Dear NAMD users,
well, this is a VMD question not really a NAMD question
> I couldn't find an answer to this on the "pbc tools" page or in the mainling list.
> I need to wrap my system around a specific origin point and x, y and z lengths (x=132, y=96, z=110).
>
> I have been trying such commands as:
> pbc wrap -orthorhombic {132, 96, 110} -center {0 0 0} -sel "all"
> but get:
> pbcwrap: unknown option: 132, 96, 110
and rightfully so, as this does not make sense and is
in violation of the documentation.
if you want to wrap around {132 96 110} you should use
that as argument to -center.
also, please note, that tcl lists/vectors have no comma.
axel.
> I have also tried other variations but none have worked.
> What correct form/command should I use?
>
> Thanks in advance
>
>
>
> Elia Zomot, PhD
> Computational and Systems Biology Department
> School of Medicine, University of Pittsburgh
> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
> Voice: 412 648 7785 - Fax: 412 648 3163
> enz1_at_pitt.edu
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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