Yes it will decompose that way, but you need to realize that the infinite,
periodic electrostatics are in there as well.
On Tue, Sep 3, 2019 at 5:26 PM Song, Lin <songlin3.chemistry.msu.edu> wrote:
> Thanks, Dave!
>
> I actually meant to say all the other electrostatic energies besides the
> 1-4 ELEC. The atom pairs that are more than 3 bonds away are counted and
> the electrostatic energies are summed up. Is this correct as well?
>
> Best,
> Lin
>
> > On Sep 3, 2019, at 5:08 PM, David Cerutti <dscerutti.gmail.com> wrote:
> >
> > That's how it is calculated. The sander and pmemd programs read a list
> of
> > 1-4 interactions from the topology file, compute the scaled ELEC and VDW
> > terms, and make running sums of those energies. The mdgx program looks
> at
> > the topology and decides for itself which atoms are separated by exactly
> > three bonds, no more, no less. The results should be identical--the only
> > case where I've seen them differ are cases where the non-tleap topology
> had
> > it wrong (double-counting some 1-4s), which sander and pmemd did not
> check.
> >
> > Dave
> >
> >
> > On Tue, Sep 3, 2019 at 3:09 PM Song, Lin <songlin3.chemistry.msu.edu>
> wrote:
> >
> >> Hi Dave,
> >>
> >> Thanks for the info! I have one more question related to this. Is the
> ELEC
> >> energy (generated by AMBER using the following input file) calculated by
> >> the this way: first, count all the atom pairs that are 3 bonds away from
> >> each other; second, calculate each pair’s electrostatic interaction and
> sum
> >> them up?
> >>
> >> AMBER input file.
> >> &cntrl
> >>
> >> imin=1,maxcyc=0,igb=0,
> >>
> >> ntb=0, cut=9999,
> >>
> >> /
> >>
> >>
> >> Best,
> >> Lin
> >>
> >>
> >>
> >>
> >>> On Aug 30, 2019, at 12:59 PM, David Cerutti <dscerutti.gmail.com>
> wrote:
> >>>
> >>> The point of a pair list is to cull the total number of non-bonded
> >>> interactions based on the arrangement of the system in space at a given
> >>> time, so there would be no way for ParmEd to do it. To print them with
> >>> pmemd, you'd need to go into the inner loop and shout every time it
> did a
> >>> pair. In pmemd.cuda, you'd need to allocate a big array and write to
> it,
> >>> incrementing a counter atomically, every time any thread performed an
> >>> interaction in kNLCPNE.h (and there are three places in that file where
> >> it
> >>> might perform such an interaction). Then you'd need to download the
> >> array
> >>> from the device and print it with the CPU. The program does not store
> an
> >>> enumerated list of non-bonded interactions, but rather a list of
> particle
> >>> groups that are likely to interact with one another. The non-bonded
> VDW
> >>> and ELEC energies, however, are already output is the mdout,
> partitioned
> >>> into 1-4 non-bonded and "all other (including Ewald reciprocal space
> >> sum)"
> >>> energies.
> >>>
> >>> Dave
> >>>
> >>>
> >>> On Fri, Aug 30, 2019 at 12:40 PM Song, Lin <songlin3.chemistry.msu.edu
> >
> >>> wrote:
> >>>
> >>>> Hi all,
> >>>>
> >>>> May I ask if there’s a way to print all the non bonded pair list and
> >>>> corresponding VDW and ELEC energies? Given the prmtop and inpcrd
> file. I
> >>>> know Parmed can print out all the bond, angle and dihedral info, but
> not
> >>>> sure about the non bonded pairs.
> >>>>
> >>>> Thanks!
> >>>>
> >>>> Best,
> >>>> Lin
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>>
> >>
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Received on Tue Sep 03 2019 - 16:00:02 PDT
