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
binding_energy.log
mdinfo
restrt
snapshot_lig.all.out
snapshot_statistics.in
snapshot_rec.all.out
snapshot_com.all.out
sander_com.in
sander_lig.in
sander_rec.in
Decomp_Residue.mmpbsa
Other than snapshot_statistics.out, anybody could help me regarding
this.
Thanks in advance,
Sincerely,
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Robert Duke
Sent: Thursday, May 10, 2007 11:46 PM
To: amber.scripps.edu
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
es_cutoff,
and cut should then not be specified. This is one way to get increased
vdw
accuracy and retain a lower cost on the electrostatics. I designed this
to
answer the "need", real or perceived, to go to 9 or 10 angstrom cutoff
for
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
pain.
It is a small optimization to use es_cutoff 8, vdw_cutoff 9, but
apparently
there is some enthusiasm out there for doing this. All this is
practical
with tip3p water essentially because vdw calcs only need to be done on
1/3
of the solvent atoms and the solute.
Regards - Bob Duke
----- Original Message -----
From: "Thomas Cheatham" <tec3.utah.edu>
To: <amber.scripps.edu>
Cc: "Ross Walker" <ross.rosswalker.co.uk>
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.
Now,
>> my
>> understanding is that the higher the cutoff value the more accurate
the
>> 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
electrostatics
> with Ewald or particle mesh Ewald; if you were to run a straight
cutoff
> simulation, then yes, one might think that making the cutoff larger
will
> 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
Steinbach
> and more recent ones by Daggett and others that provide the gory
details.
>
> With Ewald, it is all about the balance. The direct space (i.e.
within
> the cutoff) and the reciprocal (effectively what is missing for the
true
> periodic image) need to be balanced in term of their accuracy. It is
not
> formally correct to think of the direct as short range and the
reciprocal
> 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
accurate
> this is. The higher the accuracy and shorter the cutoff means that
you
> have to put more accuracy into the reciprocal sum to compensate;
either
> more lattice vectors in Ewald, or finer grid, higher interpolation in
PME.
> If you want to run a 20A cutoff fine, then you can run a not so
accurate
> reciprocal and get equivalent answers. The problem with this is that
the
> 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
uniform
> density approximation to partially correct...
>
> Short summary: Bigger isn't necessarily better; you want balance
between
> the two terms. You can check accuracy by increasing DSUM_TOL and/or
grid
> 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
