I already manually edited the prmtop file and removed the dihedral items
that have zero force constants. Then, the problem has disappeared.
On Fri, Jul 30, 2010 at 9:41 PM, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Jul 30, 2010, InSuk Joung wrote:
> > if( uv == 0. ){ /* or maybe uv < 1.d-10 or something? */
> > co = 1.0; /* or maybe something else?? */
> > } else {
> >
> > Isn't this necessary above?
> > den = 1.0
>
> Yes. I didn't have the code in front of me, and didn't see that den is
> used elsewhere.
> >
> > Otherwise, den is an arbitrary number. I am not sure whether it will
> cause
> > a problem.
> >
> >
> > Also, similar things are in sff2.c
> >
> > line 1265:
> >
> > assert(bi > 0.01);
> > assert(bk > 0.01);
> >
> > Is this really necessary?
>
> I think something is necessary if you really must have bond angles of 180
> degrees. The diehedral angle (and hence its derivative) is undefined
> there.
> Instead of triggering an assert, one could put in dummy values (as I
> suggested
> in eff.c), on the assumption that everything will be multiplied by zero
> later
> on anyway. But we might really want to think about having leap strip out
> zero force constant diehedrals before the prmtop is written, so that this
> problem never comes up....that would be a better solution, since otherwise
> the sff code would have to double check that the force constant really is
> zero.
>
> ....dac
>
>
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--
Best,
InSuk Joung
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Received on Fri Jul 30 2010 - 19:00:05 PDT
