RE: AMBER: &dipoles in sander

From: Ross Walker <>
Date: Fri, 28 Jan 2005 10:10:21 -0800

Dear Jenk,
> Is it possible to measure inducable dipoles in
> implicit solvent environments rather than polarized
> explicit solvent environments ?

In terms of how &dipoles is implemented in the code yes it is. If you run an
inducible dipole simulation (ipol=1) then the contents of the inducible
dipole array, the array that sander uses during an inducible dipole MD
simulation, for the groups you select will be printed. What this means
'physically' I am not entirely sure. I haven't tried running inducible
dipole simulations with implicit solvent so I don't know how well they work.
Perhaps a GB expert on the list can comment more on this.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Jan 28 2005 - 18:53:00 PST
Custom Search