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

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Apr 24 2011 - 13:00:10 CDT

On Sun, Apr 24, 2011 at 1:51 PM, Zumot, Elia Nabil <enz1_at_pitt.edu> wrote:
> I have read the manual, downloaded vmd 1.9, copied pbcwrap.tcl and all relevant files to the working directory and followed the exact directions mentioned:
>
> % source pbcwrap.tcl

NOOOOOO!!!!!!

pbcwrap.tcl is obsolete!!!
the functionality is part of the pbctools plugin and
comes pre-packages with VMD. no additional
installation is needed.

> % pbcwrap -sel "all" -xst test.xst -first 0 -last last

>
> but got the following:
> """
> PBCwrap log
> ===========
> Reading unit cell info from XST file:
> test.xst
> invalid command name "set_unitcell_xst"
> """
>
> and no output was generated

sorry, but GIGO. no surprise here.

axel.

>
>
> 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: Saturday, April 23, 2011 4:37 AM
> 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 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.

-- 
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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