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
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Received on Tue Sep 03 2019 - 14:30:03 PDT
