I wrote:
> Therefore you need to choose a novel atom
> type for the new hydrogen and assign it parameters that
> are correct on the bonded side and 0 on the disappeared-
> bond side.
Dave Case wrote:
> The bond and angle terms keep the dummy atom near to the
> positions they have in the real system, and hence generally
> enhances sampling.
Note that you need your ring to open freely, so if I have
interpreted the problem correctly the only dummy atoms will
be the h's attached to the mutated c that becomes an h. As
Dave points out, it is good to keep these dummy atoms in a
reasonable position relative to the h they are attached to.
Once your ring has opened, it may be hard to get it to close
on the reverse path, e.g. it might be impossible or yield
very high energy if the h-n bond happens to pass through the
center of a ring as it switches from 0 to full potential c-n.
Bill
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Received on Tue May 18 2004 - 00:53:01 PDT
