Re: AMBER: cyclohexane and decalin on amber

From: FyD <>
Date: Sun, 30 Sep 2007 09:20:29 +0200

Quoting Jones de Andrade <>:

> 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.
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:

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
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