Re: [AMBER-Developers] [ redundantredundancies]

From: Robert Duke <>
Date: Mon, 13 Jun 2011 23:51:41 -0700

Hi Jason,
On fft's in pmemd, my adapted version is pretty darn fast and portable
(original source was netlib, first adopted by Darden, and then I did a
substantial rewrite that made it faster), and you don't have to use any
external libraries. I don't think you were suggesting discarding it, but I
wanted to be sure it is understood that it really does a pretty good job.
For the fftw stuff, it CAN be a bit faster on some machines, especially at
very low processor count, but is a bigger pain to build, and as you scale up
in processor count, it does not make much difference. There are two
versions because there were two extant versions of fftw at the time of
development, incompatible with each other, and everyone had not moved
forward to the second version. I suppose one could get rid of the older
version, but it is not as if there is a huge benefit in doing this. In
pmemd, the interface to the fft's has been generalized, making it easy to
add new fft implementations; this also means that there is little cost in
having a few extra implementations lying about.
Regards - Bob Duke

----- Original Message -----
From: "Jason Swails" <>
To: "AMBER Developers Mailing List" <>
Sent: Monday, June 13, 2011 10:05 PM
Subject: Re: [AMBER-Developers] [

> Hello everyone,
> The descriptions for each program are done (but only for AmberTools 1.5,
> none introduced since then). It is now Chapter 2 of the AmberTools
> manual,
> and is part of the master branch. Please feel free to improve the
> (short!)
> description for your program(s).
> tleap/sleap, cpptraj/ptraj, and are obviously 3 of
> the
> big ones.
> For cpptraj/ptraj, I think cpptraj offers something new over ptraj that
> makes it worth keeping, but ptraj does too much to discard at this point.
> I
> support keeping both here.
> For tleap vs. sleap; I'm not quite sure what the design goal for sleap was
> in the first place (as I wasn't around when it was begun), but it appears
> to
> be a bit buggy, and with no GUI version available, people will probably
> continue to use tleap/xleap. I don't think we can get rid of tleap (at
> least not at this point).
> For, I'll obviously support our version, and it does
> everything the perl version does as well as MM/3D-RISM and QM/MMGBSA if
> one
> isn't built.
> Onto some of the smaller ones, here are the redundancies I found:
> / top2ff : produces a complete frcmod
> along with LJ non-bonded terms.
> ambpdb / top2mol2 : ambpdb does what top2mol2 does as well as prints out
> other formats (PDB, PQR)
> reduce / protonator : based on descriptions I found, reduce does what
> protonator does and more
> mmE / NAB, sander, pmemd, mdgx : I'm not quite sure what sets mmE apart,
> although it may just be an example program using MTK++
> sequenceAligner/superimposer : It seems that superimposer just does part
> of
> what sequenceAligner does? Perhaps Martin can clarify here a little?
> Some more redundancies: we have Bob's pubfft (?) used in pmemd, as well as
> 2
> versions of fftw (2.1.5 and 3.2.2).
> All the best,
> Jason
> On Mon, Jun 13, 2011 at 8:16 PM, case <> wrote:
>> I agree with Jason's comments below. I'm happy to let him get started as
>> proposed, but I hope everyone will help out in working on simplification.
>> There are both types of issues outlined below, plus much bigger issues,
>> e.g.:
>> tleap vs sleap
>> ptraj vs cpptraj
>> python vs perl versions of mm-pbsa
>> I don't have any magic answers, but cleanup and simplification of both
>> code
>> and documentation should be a high priority for the next release.
>> [On Jason's specific points, we can probably retire top2mol2, top2ff,
>> and maybe some of the other minor antechamber scripts.]
>> ...dac
>> ----- Forwarded message from Jason Swails <> -----
>> Date: Mon, 13 Jun 2011 14:53:59 -0600
>> Subject: redundant redundancies
>> From: Jason Swails <>
>> I'm going through Amber and AmberTools right now and adding a section of
>> the
>> manual that more or less lists all of the programs that exist in each
>> package right now that gives a short (1-sentence) description of its
>> functionality and where in the manual you should look for its
>> description.
>> In doing so, though, I've found numerous redundancies. For instance:
>> and top2ff do the same thing (although the first one
>> provides a more complete FF file from a given prmtop). top2mol2 mimics
>> ambpdb with the -mol2 flag. I can provide a more complete list after I'm
>> done, though I think we should start thinning out the number of provided
>> programs; at the very least eliminating redundancies. There are 97 (!)
>> programs installed with AmberTools (just serial).
>> Thanks!
>> Jason
>> ----- End forwarded message -----
>> _______________________________________________
>> AMBER-Developers mailing list
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER-Developers mailing list

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Received on Tue Jun 14 2011 - 00:00:04 PDT
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