From chemistry-request "-at-" ccl.net Mon Jul 27 17:38:50 1992
Date:    Mon, 27 Jul 1992 12:16:44 -0700 (PDT)
From: F0418950 "-at-" JAGUAR.CSC.WSU.EDU
Subject: Periodic Boundary Conditions in DISCOVER
To: chemistry ^%at%^ ccl.net
Status: R


Help!

Has anyone successfully carried out a MD simulation with peroidic boundary
conditions (pbc) using the AMBER ff in DISCOVER 2.8.0 (by Biosym)?
I would like to solvate a molecule I have and carry out a pbc md simulation
.  At the moment I have been just trying to get a pdc md simulation to work
on a 10 angstrom cubic box without success.
The directions in the manual are sketchy at best, especially in its 
description of the requirements for a pbc calculation( i.e. it states that
after a pdc solvation has occured the replicate molecules must be made into
real molecules and all replicates of the solvated molecule must be placed
explicitly in the unit cell - - - say what?).
Any help or examples(and clairification) would be greatly appreciated.


Thanks in advance,

Andrew 
f0418950 ":at:" jaguar.csc.wsu.edu
Washington State University
Dept. of Biochemistry

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