AMBER: binding energy_decomposition per residue

From: Srinivas Odde <>
Date: Fri, 11 May 2007 16:39:50 -0500

Dear Amber Users,

I have some error while doing decomposition per residue calculations. I
got error something like this

Missing BELE for MM in 1 (residue 1)

I got all the files

Other than snapshot_statistics.out, anybody could help me regarding

Thanks in advance,


-----Original Message-----
From: [] On Behalf
Of Robert Duke
Sent: Thursday, May 10, 2007 11:46 PM
Subject: Re: AMBER: Sander (Amber 9) crash on cortex

With pmemd 9, you can now run a larger vdw cutoff than electrostatic
cutoff - the mdin &cntrl namelist variables are vdw_cutoff and
and cut should then not be specified. This is one way to get increased
accuracy and retain a lower cost on the electrostatics. I designed this
answer the "need", real or perceived, to go to 9 or 10 angstrom cutoff
vdw while not having the cost of increasing electrostatics cutoff in pme

past 8 angstrom. One could use shorter electrostatic cutoffs than 8; I
personally found balancing the error - basically figuring out how to
increase the reciprocal space accuracy to compensate, to be a bit of a
It is a small optimization to use es_cutoff 8, vdw_cutoff 9, but
there is some enthusiasm out there for doing this. All this is
with tip3p water essentially because vdw calcs only need to be done on
of the solvent atoms and the solute.
Regards - Bob Duke

----- Original Message -----
From: "Thomas Cheatham" <>
To: <>
Cc: "Ross Walker" <>
Sent: Thursday, May 10, 2007 10:56 PM
Subject: Re: AMBER: Sander (Amber 9) crash on cortex

>> simulation with cut=10 and it ran successfully. So, this is a fix.
>> my
>> understanding is that the higher the cutoff value the more accurate
>> energy
>> values for the simulation. However, I understand that PME does
>> compensate for
>> the cutoff. In your opinion, will the change from cut=10 from cut=20

>> make
> This is not entirely correct, at least when talking about
> with Ewald or particle mesh Ewald; if you were to run a straight
> simulation, then yes, one might think that making the cutoff larger
> lead to better behavior. This too is an erroneous assumption due to
> fortitous cancellation of error. There are a number of earlier papers
> that discuss these issues, a classic being Steinhauser on peptide
> simulation.
> If you are using a cutoff, then this should be smoothed or shifted in
> terms of the energy or force; there are classic's by Brooks and
> and more recent ones by Daggett and others that provide the gory
> With Ewald, it is all about the balance. The direct space (i.e.
> the cutoff) and the reciprocal (effectively what is missing for the
> periodic image) need to be balanced in term of their accuracy. It is
> formally correct to think of the direct as short range and the
> as long range, although this is often done. In each case, the term is
> smoothed in some manner. In the case of the direct sum, within the
> cutoff, this is smoothed by the erfc() which brings the terms close to
> zero at the cutoff. In AMBER you can set DSUM_TOL to control how
> this is. The higher the accuracy and shorter the cutoff means that
> have to put more accuracy into the reciprocal sum to compensate;
> more lattice vectors in Ewald, or finer grid, higher interpolation in
> If you want to run a 20A cutoff fine, then you can run a not so
> reciprocal and get equivalent answers. The problem with this is that
> direct part costs significantly more in terms of computer time so you
> are shooting yourself in the foot...
> When Ross Walker mentioned 8-10A, this is how we have balanced both
> accuracy and performance with PME with default parameters. We could
> probably go to even smaller cutoffs (with better runtime performance)
> however we need to worry about vdw too... These cannot be run at 6 A
> cutoff accurately (and keeping two pairlists kills the speed advantage
> somewhat); 8-10A is pushing it, although in AMBER you can apply a
> density approximation to partially correct...
> Short summary: Bigger isn't necessarily better; you want balance
> the two terms. You can check accuracy by increasing DSUM_TOL and/or
> density, interpolation order, etc. We tend to try to run with force
> errors on the 10**-6 range, i.e. pretty small. A good test is energy
> conservation (as you alter the variables in NVE simulation).
> Good luck with your protein structures.
> -- tec3
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Received on Sun May 13 2007 - 06:07:39 PDT
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