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

From: Zumot, Elia Nabil (enz1_at_pitt.edu)
Date: Sun Apr 24 2011 - 14:44:06 CDT

Thanks for the help Axel but its still not working.
This time I didn't copy any tcl scripts, simply loaded the psf and dcd files and just used (as specified in the manual):

% pbc readxst test.xst
% pbc wrap -sel "all" -all
Info) 0.6% complete (frame 0)
..
Info) 100.0% complete (frame 175)
%

There was no output file but the whole structure was just smeared (stretched-bonds).
So since in my simulation only water molecules were wrapped (and not the lipids or protein), I tried unwrapping everything and then wrapping all but again:

% pbc unwrap -sel "all" -all
Info) 1.1% complete (frame 1)
Info) 2.3% complete (frame 3)
Info) 3.4% complete (frame 5)
....
Info) 84.1% complete (frame 147)
Info) 92.0% complete (frame 161)
Info) 100.0% complete (frame 175)

% pbc readxst test.xst
% pbc wrap -sel "all" -all
Info) 0.6% complete (frame 0)
Info) 13.6% complete (frame 23)
...
Info) 100.0% complete (frame 175)
%

and the result was the same smear and no output file

Thanks

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: Sunday, April 24, 2011 2:00 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 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pbcwrap.tcl is obsolete!!!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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