AMBER Archive (2006)

Subject: RE: AMBER: a question

From: Ross Walker (
Date: Fri Apr 21 2006 - 15:35:51 CDT

> I'd like to know if anyone knows, how the PME works..

Nope, none of us have a clue... It is just voodoo magic ;-)

> I have a technical question regarding PME...
> Is the value of CUT the cut off value only for VdW forces in
> the direct (r) space? and are only the electrostatic forces (EF)
> treating in the k space? or are VdW and EF cutoff in the r space and some

> contribution of the EF is considered in the k space?

The final sentence is the correct one:

cut specifies the real space cut off of both the VDW and Electrostatic
interactions. An error function (erfc) is then used to remove overcounting
of the electrostatic interaction that would occur in the reciprocal space.
This function is adjusted to match the value of cut. Values of cut below 8
angstroms however are not appropriate because this would truncate the VDW
interactions too early. As I mentioned in a previous email recently
implementing a separate electrostatic and VDW cutoff would not gain you any
performance benefit so it is best to use the appropriate value for
truncating the VDW interaction as the value for truncating the real space
electrostatic interaction.

For more details I would refer to references 73 to 76 in the Amber 9 manual

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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