Hi everyone,
This is a rather technical discussion regarding the 1-4 nonbonded
interactions and how they are computed differently for sander and pmemd.
In particular, sander uses the following logic to identify 1-4
interactions for the L-J and electrostatic loops:
if ( (k >= 0) .and. &
(l >= 0) .and. &
(.not. qmmm_skip) &
)then
l<0 indicates an improper torsion and k<0 indicates end-groups are
ignored (e.g., for multi-term dihedrals and ring systems). qmmm_skip
indicates this pair is in the QM region, which is all well and good. By
contrast, pmemd has:
if (gbl_dihed(dihed_idx)%atm_k .gt. 0 .and. &
gbl_dihed(dihed_idx)%atm_l .gt. 0 .and. &
gbl_fmn(gbl_dihed(dihed_idx)%parm_idx) .ne. 0.d0) then
where gbl_fmn is basically a boolean mask array that is set to 1 when
the dihedral periodicity is nonzero and 0 otherwise. In practice, there
is no harm in ignoring dihedrals whose periodicities are 0, since they
add a constant shift to the energy (and by extension no contribution to
the force). But the dihedral list in Amber serves a dual purpose -- it
is both the list of torsion parameters in the system *and* the source of
the 1-4 nonbonded pairlist. When porting other force fields to work
with Amber, some programs make use of 0-periodicity torsions
specifically to tag nonbonded pairs -- a scenario that sander gets
correct and pmemd currently gets wrong.
My inclination is to simply get rid of gbl_fmn altogether (since it
*only* serves to ignore 1-4 nonbonded pairs that should, it seems, never
be ignored). Since this seemed deliberate, though, I wanted to know if
anybody had insight into why pmemd behaves the way it does, and if there
is anything I'm missing in my analysis that makes this proposal
dangerous. But at the very least, we should make sure sander and pmemd
do the same thing.
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 18 2015 - 07:00:03 PDT
