Subject: MD in Tinker

From: Andreas Goeller <[email-masked]>
Date: Tue, 11 Jul 2000 10:20:19 +0200

Dear CCLers,

I already worked through the manual and know how to wrtie inputs, start
jobs etc in tinker.
But I need help in setting up a reasonable input for MD simulations of 

1) an organic molecule in gas phase
2) the same molecule in a solvent box

The following problems arise:

1) how does an input for MD look with reasonable choices ( NVE, T=300K,
p= 1atm)
2) how to place the molecule in the water box (i.e. generate the
xyz-file)
3) which solvents are readily accessible (I know of Tip3e water), how do
I define
   the different parameter sets for organic molecule and water
4) how do I analyze a variable like say a torsion from the output I get?
Can I define
   it in any way and monitor it?

I would greatly appreciate any working input examples (best with
comments) which will
help me. I would summarize the results

-- 
                                Andreas Goeller

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   Dr. Andreas Goeller       Institut fuer Physikalische Chemie
                               Friedrich-Schiller-Universitaet
                                       Lessingstr. 10
phone: +49(0)-3641-948352               D-07743 Jena
  fax: +49(0)-3641-948302 (secretary)     Germany
email: [email-masked]
http://www.uni-jena.de/chemie/photo/goeller/goeller.html
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   Dr. Andreas Goeller   ehemals Computer Chemie Centrum

email: [email-masked]
http://www.organik.uni-erlangen.de/clark/goeller/goeller.html
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