[EMAIL PROTECTED] wrote:
There's no a priori reason why a mixture of a united-atom detergent
sodium dodecyl sulfate and an all-atom peptide *couldn't* work.
Neither is there any reason to suppose they *would* work without
evidence that the SDS parameters were developed with this purpose in
mind and suitably validated. For that, you'll have to read the paper
referred to on the page you footnoted [1], I guess. Your other
alternative is looking for an all-atom SDS topology that has been
validated, but I've no idea whether one exists.
Do you have any suggestions how one would validate the combination of
two such force-fields? While generally one could always develop new
parameters using the same methodology as the existing forcefield, it is
not obvious how one would do this when combining all-atom and
united-atom representations.
No, I don't have specific ideas - I've never considered the issue. All I
think that one could do is to make the decisions for that particular
combination in a way that might be thought sensible, and to test the
results against experimental data.
I see how the basic combination rules, etc. could be validated by
simulating for example an aqueous protein restrained to one half of the
simulation box and an SDS micelle restrained to the other half of the
box in order to ensure no vdw contacts and then compare equilibrium
properties from this simulation to those of an aqueous protein and an
SDS micelle in separate simulations.
Hmmm, if you've arranged no vdw contacts between the two pieces of force
field, then you're really not testing anything much with the above.
However failure with the above should indicate you should go and work on
something easier, like modelling brain function. :-)
Further, in some situations one could look at the parameters to see the
there are no striking differences between similar atom types. This would
definitely be useful for example when trying to combine an all-atom
protein forcefield with a united-atom forcefield. However, SDS doesn't
really have any groups that are similar to and protein groups. Further,
it is not readily apparent to me how one would even extend a protein
forcefield using the same methodology to SDS and be sure based simply on
methodology of generation that they were valid in combination since
there is so little overlap in actual group types.
True.
Mark
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