the key issue to me is not whether the list is supplemented
but whether the content in the prmtop is ever discarded.
I think that is what Yong initially suggested, and it's still not
clear from these emails if part of the code is doing this or not.
If someone doesn't want to use the prmtop list, they should
be very careful in assuming that they know how it was built.
For example, just because someone thinks that exclusions
are for 1-2, 1-3 etc doesn't mean that you can just redo it
that way. I think that this is a general concern- we really
should not make any assumptions these days about what
is "typical" or how something works without warning
everyone else. Other developers are using the code in
ways that are very different from a "traditional" MD
simulation and assumptions about how the code runs or
even what a "molecule" is can be dangerous. This
doesn't have much to do with file formats, it's much
more about assumptions about what the user's system
must be.
having said that, the best way to avoid problems is probably
for us to write test cases that will break if someone makes
incorrect assumptions. I'm not great about that myself,
but it's probably the only practical way to protect our own areas
of the code these days. dac has been saying that for a while now...
carlos
Received on Wed Apr 05 2006 - 23:49:49 PDT
