Re: AMBER: cyclohexane and decalin on amber

From: Jones de Andrade <>
Date: Mon, 1 Oct 2007 02:46:44 -0300

Hi François.

Thanks a lot for thelinks and reference. I guess they will be helpfull.

Can I make one question? Well, unfortunatelly I could not yet get access to
the reference you sent me (will have to get in touch with the author for
this specific one). But, from what I could get from its abstract, it was not
fairly easy to reproduce the eectrostatic potencial around a simple molecule
like cyclohexane with only simple atomic point charges.

I wonder what would lead to such a difficult on simple alcanes for that.
Specially considering the "trick" used of placing extra punctual charges in
midle of the hidrogens. I would not in a first instance expect such problems
on such simple molecules. Could you please give me any indication of what
sort of molecule "characteristic" or "property" would lead to such problems?
I still wandering what would be a good reason for that, even considering
some kind of "polarizability effect" that first came to my mind, but I'm
absolutelly unsure on this.

Thanks a lot in advance for all help! ;)

Sincerally yours,


On 9/30/07, FyD <> wrote:
> 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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Oct 03 2007 - 06:07:14 PDT
Custom Search