AMBER Archive (2006)

Subject: Re: AMBER: a question

From: Robert Duke (
Date: Mon Apr 24 2006 - 13:21:34 CDT

There actually is a slight performance benefit (say if you were to make the
es cutoff 8 A and the vdw cutoff 9 A instead of making them both 9) and what
you get is numbers for vdw closer to 9 A cutoff numbers, about the same es
numbers, and a calculation time intermediate between the time for es/vdw
cuts of 8 vs. es/vdw cuts of 9 angstrom. PMEMD 9 is capable of doing this
with the new mdin cntrl keywords es_cutoff, vdw_cutoff. The performance
advantage is small enough I have not made a big deal about it, but do
document stuff in the amber 9 manual (your perspective here has to be that
you want better vdw numbers but want to slightly reduce the cost).
Regards - Bob Duke

----- Original Message -----
From: "Ross Walker" <>
To: <>
Sent: Friday, April 21, 2006 4:35 PM
Subject: RE: AMBER: a question

>> 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
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
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