[DFTB-Plus-User] Geometry optimizations with PBC

[Jerry Tanoury]

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

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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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