Re: pbc wrap option for x,y,z lengths

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Apr 23 2011 - 03:37:20 CDT

On Fri, Apr 22, 2011 at 11:52 PM, Zumot, Elia Nabil <enz1_at_pitt.edu> wrote:
> 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)?

of course not!

>
>> 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.

that is different from what you wrote.

> This one doesn't work either:
>
> % pbc wrap -orthorhombic {132 96 110} -center {0 0 0} -sel "all"

of course not, that is the same you wrote before. the -orthorhombic
flag does _not_ take any argument. you have to _read_ the pbctools
documentation. obviously you have only glossed over it.

pbctools assumes that the periodic cell _dimensions_ were
already given with the trajectory file and thus available internally
to VMD. if that is not the case, you need to set this either via
reading the data from a file or set this manually with the pbc set command.

do a proper RTFM and you will see.

axel.

> 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.

-- 
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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