VMD-L Mailing List

From: Yann Claveau (yann.claveau_at_univ-rennes1.fr)
Date: Wed May 12 2021 - 08:29:46 CDT

Indeed, using "$selSi set name 1Si" works, thank you very much !

I definitely don't like pdb format but a lot of old tools use it.
Hopefully there is topotools ! ^^

Le 12/05/2021 à 15:20, Axel Kohlmeyer a écrit :
> if I remember correctly (it is about 10 years since I wrote that
> code), topotools doesn't use the "name" property, but the "type"
> property of selected atoms.
> Since .pdb files do not provide a field for atom types (those are
> usually imported from .psf files) VMD may assign the same value to
> "name" and "type" when reading a .pdb file.
>
> On Wed, May 12, 2021 at 9:13 AM Yann Claveau
> <yann.claveau_at_univ-rennes1.fr <mailto:yann.claveau_at_univ-rennes1.fr>>
> wrote:
>
> Actually it does not work. I guess I'm doing something wrong.
>
> I use for instance
>
> $selSi set name 1Si
>
> But then, following the tutorial part 1
> (https://urldefense.com/v3/__https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1__;!!DZ3fjg!vWkS0at7W7RrSDYB_TT2o24IJZN-Gk99cn5f86QZpkd_As48MEwstDGcTKD_vDa_qQ$
> <https://urldefense.com/v3/__https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1__;!!DZ3fjg!vWkS0at7W7RrSDYB_TT2o24IJZN-Gk99cn5f86QZpkd_As48MEwstDGcTKD_vDa_qQ$ >),
> Only the orginal atomtype names are in the lammps data file.
>
> I could modify the pdb first by replacing the name (as in 1Si) but
> if there is a better way with topotools let me know.
>
> Cheers,
>
> Yann
>
>
> Le 12/05/2021 à 11:30, Axel Kohlmeyer a écrit :
>>
>>
>> On Wed, May 12, 2021 at 5:16 AM Yann Claveau
>> <yann.claveau_at_univ-rennes1.fr
>> <mailto:yann.claveau_at_univ-rennes1.fr>> wrote:
>>
>> Dear all,
>>
>> I used topotools to convert a pdb file into lammps data. I
>> would like to know if it is possible to change the numbering
>> of atoms in the lammps data file.
>>
>> Here is an example : Consider 3 atom type : H, O, Si.
>>
>> I selected them using
>>
>> set selSi [atomselect top {name Si}]
>> set selO  [atomselect top {name O}]
>> set selH  [atomselect top {name H}]
>>
>> Then, after analysis (topo retypebonds, topo guessangles, mol
>> reanalyze top) I created the lamms data file.
>>
>> topo writelammpsdata data.example
>>
>> In this file, atoms are ordered alphabetically:
>>
>> 1 H
>> 2 O
>> 3 Si
>>
>> is it possible to change this order using topotools, for
>> instance:
>>
>> 1 Si
>> 2 H
>> 3 O
>>
>>
>> the simplest way to achieve this would be by (re-)naming the
>> atoms so they will sort in the desired order, e.g. as 1H, 2O, and
>> 3Si.
>>
>> axel.
>>
>> Thanks for your help,
>>
>> --
>> Yann claveau, post-doc
>> Département Matériaux-Nanosciences
>> Bât. 11A, bureau 122,
>> Campus de Beaulieu
>> Institut de Physique de Rennes - UMR-CNRS 6251
>> Université de Rennes 1
>> 35042 Rennes cedex FRANCE
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
>> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vWkS0at7W7RrSDYB_TT2o24IJZN-Gk99cn5f86QZpkd_As48MEwstDGcTKCwKcs7qQ$ <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vWkS0at7W7RrSDYB_TT2o24IJZN-Gk99cn5f86QZpkd_As48MEwstDGcTKCwKcs7qQ$ >
>> College of Science & Technology, Temple University, Philadelphia
>> PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
> --
> Yann claveau, PhD
> Département Matériaux-Nanosciences
> Bât. 11A, bureau 122,
> Campus de Beaulieu
> Institut de Physique de Rennes - UMR-CNRS 6251
> Université de Rennes 1
> 35042 Rennes cedex FRANCE
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vWkS0at7W7RrSDYB_TT2o24IJZN-Gk99cn5f86QZpkd_As48MEwstDGcTKCwKcs7qQ$ <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vWkS0at7W7RrSDYB_TT2o24IJZN-Gk99cn5f86QZpkd_As48MEwstDGcTKCwKcs7qQ$ >
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
Yann claveau, PhD
Département Matériaux-Nanosciences
Bât. 11A, bureau 122,
Campus de Beaulieu
Institut de Physique de Rennes - UMR-CNRS 6251
Université de Rennes 1
35042 Rennes cedex FRANCE