Thanks! I ran into trouble because I was playing with extra points ...
yong
> -----Original Message-----
> From: owner-amber-developers.scripps.edu
> [mailto:owner-amber-developers.scripps.edu] On Behalf Of David A. Case
> Sent: Monday, November 14, 2005 9:55 AM
> To: amber-developers.scripps.edu
> Subject: Re: amber-developers: Excluded list ?
>
>
> On Sat, Nov 12, 2005, Yong Duan wrote:
> >
> > Can somebody out there tell me how can I
> > add a pair of atoms on the excluded atom list and expect
> sander to use it?
>
> A little trial-and-error is probably appropriate here. As
> suggested earlier
> in this thread, it looks like setting chngmask to 0 should
> turn off any new
> excluded-list generation.
>
> Looking the at the code, I see we already trap the
> combination of LES and
> extra points, printing out an error message that this is not
> supported. If
> LES is set and there are no extra points, then the exclusion
> list is *not*
> remade -- which is presumably why all the LES tests still pass.
>
> Overall, Tom did a pretty reasonable job of being careful in
> inserting the new
> code: he trapped the known options that require one to use
> the excluded list
> from the prmtop file (rather than rebuilding it), and he
> added an input option
> that disables the rebuilding anyway. A few more comments
> might have helped,
> but I'm hardly in a position to complain about that...
>
> [A question for Tom D.: is there a reason why we don't skip all the
> extra-points initialization whenever numextra = 0? That is
> have a line:
>
> if( numextra == 0 ) return
>
> at about line 198 of extra_pts.f? I know that this would
> require another
> change in the ephi() routine, but otherwise seems pretty simple. The
> objective would be to avoid running code that is not needed.]
>
> ...dac
>
Received on Wed Apr 05 2006 - 23:49:48 PDT
