Thanks everyone!
I have checked the input files and there was no 0 in the scee and scnb
parameters so Ross' answer seems to explain it well for my case.
On Wed, Nov 22, 2017 at 2:29 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Stefan,
>
> If memory serves it was added as a 'backup' check for the mechanism by
> which 1-4 interactions are handled. Sander and PMEMD handle 1-4's by
> traversing the dihedral list but obviously that means only the first
> dihedral in the series in each case should be used. The sign of the third
> index is used to handle this. Originally SCEE and SCNB factors were never
> in the prmtop - a fixed value from the &cntrl namelist was used for the
> entire calculation. When I added support for variable SCEE and SCNB values
> to properly support mixing force fields, for example Glycam with FF14SB, as
> an extra check during debugging things were setup such that additional SCEE
> and SCNB scaling factors beyond the first occurrence for a given dihedral
> would be set to zero. If the code is working correctly these values should
> never be referenced. The thought process being that if they were getting
> referenced for some reason then, since the code divides by SCEE and SCNB,
> this would trigger a divide by zero and the resulting simulation would
> yield NANs rather than what look to be potentially valid, but in reality
> incorrect, results.
>
> Hope that helps.
>
> All the best
> Ross
>
> > On Nov 22, 2017, at 05:11, Stefan Doerr <stefdoerr.gmail.com> wrote:
> >
> > Hi, I wanted to ask if there is any documentation on why tleap sets some
> > scee and scnb factors to 0. I could not find anything in the AMBER manual
> > about it. Jason Swails told me that it was used as a convention for
> > omitting 1-4 interactions but afaik the sign of the third index of a
> > dihedral already is used to indicate that:
> >
> > http://ambermd.org/formats.html
> > "If the third atom is negative, this implies that the end group
> interations
> > are to be ignored."
> >
> > Best,
> > Stefan
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>
>
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Received on Wed Nov 22 2017 - 07:30:04 PST
