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New Template from Scratch

Posted: Tue Aug 17, 2021 8:52 pm
by jdandrade

I'm following the instructions found in an online manual at ... gines.html to try to hand develop a new template for gromacs use within webmo.

I chose to use the tinker (and vasp) template files as a basis for modifications. However, I already have two main doubts (concerning tmpl files exactly):

1) In both templates it mentions the generation of different input files needed (in vasp, kpoints and poscar files, and in tinker, keyword, interactive and run files). That is extremely useful for my attempt, however I don't seem to find now to properly control the naming of these files created in each section of the template. Any suggestions?

2) In order to run gromacs, most times there is need for a preprocessing of the input files, generating a binary input file, before a second stage where the calculation is actually ran. I'm supposing I can run both processes, one immediately after the next, setting both commands in what the tinker template calls "run file".

Thanks a lot for any advise!

Re: New Template from Scratch

Posted: Wed Aug 18, 2021 1:07 am
by schmidt
Excellent questions. Note that this will be a bit tricky, since the paradigms with MD are a bit different than electronic structure codes. That said, it should be possible if you set some realistic expectations. To your queries:

1) The various extensions ( are specified as arguments to the submit_enginge_job function, as a colon (:) delimited list. In the case of VASP, symlinks are made since VASP is particular about the name (e.g. KPOINT -> input.kpoints).

2) In this case, I would just use the run_gromacs.cgi script to automatically run the sequence of commands that is required. Unless there is need to customize this sequence based on the particular job, this can simply be hard coded rather than specified in the template.