On Tuesday 15 June 2010 11:31:16 Ross Walker wrote:
> Hi Thomas,
>
> Just so I understand this properly. The chamber patch will take the
> polarizability data from the charmm force field file and include it in the
> prmtop file. Are the implementations of the polarizable force fields in
> charmm and amber identical?
Polarizabilities are identical (Angstrom³)
> Can you just confirm that you tested things in the same way we tested
> things with chamber in the first place. That is run both charmm and amber
> with the charmm_dump_gold flag set and confirm that when ipol=1 in amber
> (and whatever the setting is for a polarizable simulation in charmm) you
> get identical answers (to machine precision) for a single point energy
> calculation. Both the energies and forces should match to machine
> precision.
I would like to but,
-) even though my CHARMM is reasonably up to date, I find myself unable to use
the frcdump command (does one have to specify a certain keyword at compile
time or something?)
-) the only polarization method available in both AMBER and CHARMM are
inducible dipoles, however the CHARMM version cannot work with Ewald and as I
understand it AMBER cannot work without it
-) also if I am not mistaken pmemd cannot use polarisable force fields other
than amoeba, or so I think I remember to have read somewhere (and my tests
sure never worked, but that may be a different story)
However when polarising with induced dipoles in AMBER and with drude in CHARMM
at least mean squared displacement (of coordinates) matches reasonably well
for a large system (27000 atoms in 2000 molecules).
> Take a look in: /amber11/AmberTools/test/chamber/dev_tests for some
> examples.
> We need to confirm that charmm and amber (both pmemd and sander)
> will give identical answers when run with polarization before we can
> include this into chamber. If you can send the results directly to myself
> and Mark Williamson that would be great.
>
> Thanks for your work here.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Mag. Thomas Taylor [mailto:thomas.taylor.univie.ac.at]
> > Sent: Tuesday, June 15, 2010 1:54 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] Polarizability and induced dipoles
> >
> > Dear AMBER users and developers,
> >
> > Please find attached two patches:
> > - chamber.patch
> > - dipoles.patch
> >
> > chamber.patch:
> > The created prmtop file now always has a POLARIZABILITY flag. Either it
> > contains
> > only 0s or the polarizability data extracted from the prm file.
> >
> > dipoles.patch:
> > To calculate properties from the trajectory I require the induced
> > dipoles for
> > each atom. According to the documentation one can define groups and
> > then output
> > them to the out file or something, but I feel it should be possible to
> > store
> > them in the trajectory file along with coordinates and velocities.
> > For this purpose I have cannibalized the -mdip command line options as
> > it
> > appeared to be unused.
> > Also introduced is the parameter ntwm in the namespace control, which
> > behaves
> > for dipole archiving (storing) like ntwv does for velocities.
> >
> > Please consider incorporating parts or all of the patches into AMBER11.
> > Feel free to point out any bugs/problems/etc.
> >
> > HTH,
> > Thomas Taylor
>
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Received on Tue Jun 15 2010 - 04:00:03 PDT
