Subject: Re: CCL:Periodic Systems & Commercial Codes

From: [email-masked] (Dr. Eric P. Wallis)
Date: Thu, 22 Sep 1994 14:12:07 +0100

I use Polygraf 3.1 to do #1 and #2.  I use Polygraf to generate input files 
to my Monte Carlo code (CChAPP written at Phillips).  I can also visualize 
results from my MC runs using Polygraf.  As to #3, I obtained a fortran 
program from MSI which translates their binary trajectory files to ASCII.  
Using that program, I can writes trajectory files in the format that 
Polygraf can read.  One potential drawback with Polygraf, I think that the 
maximum number of atoms is 20,000.  You might have to check this out.  
Unfortunely, MSI has discontinued Polygraf and I don't know how easily it 
will be to do the same with Cerius2 (I haven't tried yet).  Hope this helps.
Eric  
>I would like to hear about any commercial codes that can do the following:
>
>1).  Solvate a molecule in an arbitrary box (for the purpose of setting up a
>     periodic system).
>
>2).  Able to do #1 with any solvent molecule I specify.
>
>3).  Has an openly defined molecular dynamics trajectory file format that
>     to which I can convert my MD trajectories, for the purpose of analysis
>     and visualization.  Also, must be able animate MD trajectories and
>     do some "real" analysis, like rdf, average structural properties, etc.
>
>4).  Is able to do the above on systems as large as 40K atoms.
>
>
>
>I know that Insight can do this.  How about products like CAChe, HyperChem,
>or any others out there.
>
>I have no great desire to run MD calculations with the computational
>codes that come with these packages.  Rather, I wish to interface capabilities
>1-3 with our own MD codes.
>
>
>
>
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***************************************************************
* Eric P. Wallis, Ph.D                                        *
* Computational Chemistry                                     *
* Phillips Petroleum Company       Office  (918)-661-7956     *
* 331A PL PRC                      FAX:    (918) 662-1097     *
* Bartlesville, OK 74004           email:   [email-masked]      *
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