On Tue, Nov 27, 2012 at 9:32 AM, Elise Duboué-Dijon <
elise.duboue-dijon.ens.fr> wrote:
> Dear Jason,
>
> Thank you very much for drawing our attention to this point.
> We just have one additional question: with respect to amber11, in amber12
> the
> 'rparms' common block now includes the cn3, cn4 and cn5 arrays but the
> BC_PARMR
> value has not changed. Is this normal ?
> Thank you again for your help.
>
I actually just noticed this when responding in another thread earlier
today. I'll repeat myself here since you were (understandably) most likely
not following that other thread:
If you plan to use sander.MPI, though, you will also have to change the
value of BC_PARMR from 24560 to the sum of all array lengths in the rparms
common block. (It's actually incorrect right now, it should be 30050 in
order for the 'new vdw model' to work in parallel).
However, I don't know that CN3, CN4, or CN5 are used or tested outside of
PB simulations in sander (it was a PBSA dev that added that code). Since
PB simulations don't run in parallel inside sander, this 'bug' would never
really surface.
HTH,
Jason
FWIW, I fixed that bug in the developer branch, although hopefully that
whole common block structure with hard-coded array lengths will be replaced
with variable length (dynamically-allocated) arrays for the next release.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 27 2012 - 07:30:02 PST
