AMBER Archive (2005)

Subject: RE: AMBER: &dipoles in sander

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jan 28 2005 - 12:10:21 CST

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
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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