Hi,
I have the following entry in a parmtop file of mine
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
3 6 -9 12 1
the third index indicates that the non-bonded interactions between the
1-4 atoms should not be computed (this particular torsion appears only
once in the file = single term dihedral). The dihedral is from four C
atoms in the phenyl ring of toluene adjacent to the methyl side group.
Now I understand that to allow mixed scaling the new flags %FLAG
SCEE_SCALE_FACTOR and %FLAG SCNB_SCALE_FACTOR have been introduced
some time in the past to allow explict recording of scaling factors.
This means, I think, that the fifth number above (ICP) points into the
first entry of these flags (the web documentation of the parmtop
format mentions arrays "ONE_SCEE" and "ONE_SCNB"). The values there are
not zero possibly implying that 1-4 scaling should be carried out
contrary to the negative third index.
So, obvious question: what is really going to happen? My first guess
would have been that ICP(H) overwrites the negative index and scaling is
indeed carried out in sander/pmemd.
Many thanks,
Hannes.
--
Scanned by iCritical.
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Received on Thu Sep 04 2014 - 02:00:02 PDT
