dear dave et al
Sorry I was gone and left discussion in such a mess---I was at my parents
and out of touch---I'll look the extra points over and get back to
everyone today. I need to in any case because I did a crude branch in
case of amoeba to avoid all this startup stuff--maybe there's a better way
tom
On Mon, 14 Nov 2005, David A. Case wrote:
> 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
