Quoting Jones de Andrade <johannesrs.gmail.com>:
> I'm having some problems in order to proper simulate some decalin and
> cyclohexane derivatives with amber force field.
>
> Does anybody knows about any reference where somebody performed simulations
> with those systems? I'm having some problems with both densities and
> intermolecular energies, but I'm not quite sure if it's source is on
> simulation parameters choosen, a limitation on the basic models themselves
> or in the derivations I've done.
You might look in R.E.DD.B.
http://q4md-forcefieldtools.org/REDDB/
Cyclohexane is in differents projects obtained with 1 or 2 conformations
Use the Download tool:
use for "-- Molecule name" Cyclohexane, you get three projects.
I am sure you can follow a similar strategy for decaline(s).
However, please read the "Cyclohexane" abstract carefully and look at
the RRMS value !
Read also the following publication:
http://www3.interscience.wiley.com/cgi-bin/abstract/109583172/ABSTRACT?CRETRY=1&SRETRY=0
Other publications on similar topics are available . the Bibliography
section of R.E.DD.B.
regards, Francois
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Received on Wed Oct 03 2007 - 06:07:03 PDT
