Re: amber-developers: isotropic periodic sums now in Amber 9

From: Kennie Merz <>
Date: Fri, 15 Apr 2005 11:47:12 -0700

  Does the IPS have a a surface energy correction (neutralizing
background)? I just downloaded the paper and will read through it, but
I thought I might get the answer faster.... The article is a tome!

On Apr 15, 2005, at 1:37 PM, David A. Case wrote:

> I have ported the IPS (isotropic periodic sum) code of Xiongwu Wu into
> sander
> for Amber 9. See amber9/doc/0README.WXW for information. A few notes:
> 1. I changed the variable IPSOPT to IPS.
> 2. Self-guided Langevin is not (yet) in Amber 9; volunteers are
> welcome!
> 3. Here is the literature reference:
> %A X. Wu
> %A B.R. Brooks
> %T Isotropic periodic sum: A method for the calculation of long-range
> interactions
> %J J. Chem. Phys.
> %V 122
> %P 044107
> %D 2005
> 4. There is IPS code in egb(), but it is commented out for now; what
> is
> really needed is IPS for EPOL -- without that, just doing IPS on the
> unscreened Coulomb interaction doesn't seem to make much sense (to me,
> anyway).
> 5. Tom Cheatham and I have been running this code (or the equivalent
> Amber 8
> version) on DNA and RNA, (periodic, explicit solvent simulations). It
> seems
> to give very good results. Densities are slightly (1%) smaller than
> with PME
> -- I'm still looking into that.
> 6. I modified Xiongwu's code some to speed it up, but some more
> things are
> still needed. There is a square root (in short_ene) that is not
> done
> in a vectorized fashion. Also, the eexips() routine needs to be
> parallelized. But it looks like this should indeed scale very
> well to
> lots of processors. Some current timings are here:
> (Look for ips=2 in the top two tables.)
> 7. Obviously, you should take care in using this code! Try some
> parallel
> runs comparing to regular PME: you should see pretty similar
> energies and
> structural behavior. You cannot use it
> right now for free energy perturbation (icfe=1), but that is a high
> priority of mine, since that will be key in further testing the
> extent
> to which this idea can replace PME. Some other combinations of
> parameters
> may also not work.
> 8. There are test cases in amber9/test/{gact_ips,gb_rna}
> 9. Xiongwu: thanks for providing this! Let us know if you have
> further
> experience or ideas. You might think about subscribing to the
> amber-developers list: send e-mail to, with
> "subscribe amber-developers" in the body of the message.
> ...dac
Professor Kenneth M. Merz, Jr.
104 Chemistry Building
Department of Chemistry
The Pennsylvania State University
University Park, Pennsylvania 16802


Phone: 814-865-3623
FAX: 814-865-3292
Cell: 814-360-0376
Received on Wed Apr 05 2006 - 23:49:58 PDT
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