Kennie,
IPS likes Ewald using images to represent long range interaction, but
instead of lattice images used by Ewald, IPS uses so called isotropic
periodic images so that the calculation is much easier. So no surface
correction is added.
I hope I answered your question.
Xiongwu Wu
> -----Original Message-----
> From: Kennie Merz [mailto:merz.psu.edu]
> Sent: Friday, April 15, 2005 2:47 PM
> To: amber-developers.scripps.edu
> Subject: Re: amber-developers: isotropic periodic sums now in Amber 9
>
>
> Hi,
> 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!
> Kennie
>
>
> 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:
> >
> > http://amber.scripps.edu/cgi-bin/wiki.pl/Amber_9_Benchmarks
> >
> > (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
> majordomo.scripps.edu, 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
>
> e-mail: merz.psu.edu
> http: http://merz.chem.psu.edu
>
> Phone: 814-865-3623
> FAX: 814-865-3292
> Cell: 814-360-0376
>
Received on Wed Apr 05 2006 - 23:49:58 PDT
