AMBER: RE: about PME in Amber6

From: Ross Walker <>
Date: Fri, 6 Aug 2004 11:37:06 -0700

 Dear Grace

> In a previous email I posted on the mailing list regarding
> Amber cutoffs.
> (I have a approximately 24 by 24 by 24 box with molecular
> ions solvated in
> explict TIP3P waters). You said that the CUT variable is not
> involved in
> atombased cutoffs but in truncating the direct real sums in
> the ewald sums.
> I have a few regarding how the ewald method works in AMBER.
> Is is true that the electrostatic interactions are ONLY
> computed for those
> atoms falling within the CUT and the ALL the interactions
> greater than CUT are NOT consider?

No, this is not true for a PME calculation. In a normal gas phase or
periodic simulation (NON Ewald) the cutoff is used to determine specifically
what pairwise charge and van der Waals interactions are calculated. Thus the
above statement is true for a NON ewald simulation. In the Ewald or PME case
the van der Waals terms are calculated in the same way as the non ewald
simulation with any pairs that are more than CUT angstroms apart being
ignored. However, for the electrostatics ewald essentially gives you your
electrostatics out to infinity. This works because the implementation was
designed in such a way that the direct sum tends to zero within the cut off.
The interactions out to infinity are included in the reciprocal part. What
this means is that your electrostatics will only be truncated in a PME
simulation if you set the cutoff unreasonably small (Ca. < 8 angstroms). If
you plot the electrostatic energy as a function of cutoff you should see
that it converges once the cutoff exceeds 8 angstroms or so.

> So does that mean that when I look at my data (eg. PMFs
> etc..) I should
> not consider anything beyond the CUT?

No, with a PME simulation you should consider things beyond the cutoff since
your electrostatics are calculated to infinity. Just be aware however that
your van der Waals interactions were truncated at the cutoff. However, VDW
interactions are much shorter ranged than electrostatics so the error
introduced in truncating your VDW interactions should be minimal.

I hope this helps.
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 |

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Received on Fri Aug 06 2004 - 19:53:01 PDT
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