On Mon, May 18, 2015 at 11:59 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jason,
>
> Are you sure this list comes from the prmtop?
>
It comes from the dihedral array defined in the prmtop.
> For GB simulations I think it does indeed come from the prmtop but sander
> and pmemd to the best of my knowledge for periodic simulations throws out
> whatever is in the prmtop file and instead recomputes the 1-4 list manually
> in extra points.
The 1-4 list is augmented, not thrown away. If there are no virtual
sites, the 1-4 list is copied unchanged. If there *are* virtual sites,
then the 1-4 pairs involving those virtual sites are added to the list
(because they are *not* present in the prmtop -- EPs only have bonds to
their parent atom).
> I might be confusing things here with the exclusion list but you certainly
> check.
Yes, it's the exclusion list that has this problem. The exclusion list in
the prmtop is used in GB but ignored by the PME code.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 18 2015 - 09:30:03 PDT
