[DFTB-Plus-User] Geometry optimizations with PBC

[Bálint Aradi]

Dear Jerry,

we don't have a pdb-reader in DFTB+. Currently, the two supported
formats with periodic boundary condition information are the GEN format
(GenFormat) and the VASP (POSCAR) format (VaspFormat). You would have to
convert your structure to one of the two formats.

  Best regards,

  Bálint


On 3/8/22 12:33 PM, Jerry Tanoury wrote:
> Thank you Balint.  I typically generate the starting solvent box with packmol, which gives me a pdb file.  Will that file type work, or should I stay with a gen file?
> 
> Thank you again,
> Jerry
> 
> Gerald J. Tanoury, Ph.D.
> Principal Scientific Fellow
> Vertex Pharmaceuticals
> 50 Northern Avenue
> Boston, MA 02210
> Office: 617-341-6219
> Cell: 508-740-4986
> jerry_tanoury at vrtx.com
> www.vrtx.com
> 
> -----Original Message-----
> From: DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> On Behalf Of Bálint Aradi
> Sent: Tuesday, March 8, 2022 4:59 AM
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] Geometry optimizations with PBC
> 
> CAUTION: This email originated from outside of Vertex. Do not open links or attachments unless you know the sender and believe it is safe.
> 
> 
> 
> Dear Jerry,
> 
> the problem is, that you can not combine XyzFormat with LatticeVectors and Periodic. When XyzFormat is specified, it must contain valid xyz-formatted data, but no further keywords. And unfortunately, there is no standardized way to specify periodicity in the xyz-format.
> 
> Probably the easiest workaround is to write your lattice vectors as a
> 3x3 matrix in a file (e.g. latvecs.dat) and convert your geometry with
> 
> xyz2gen -l latvecs.dat Complex_MgCl2_RR-solvated.xyz
> 
> from the xyz format to the gen format, which has a standardized way to contain periodicity information. And in the input, you would then need
> 
> Geometry = GenFormat {
>   <<< Complex_MgCl2_RR-solvated.gen
> }
> 
> The xyz2gen script is part of the dptools (dftbplus-tools) package.
> 
>   Best regards,
> 
>   Bálint
> 
> --
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of Bremen http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> 
> 
> 
> 
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-- 
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/


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