On Tue, Dec 06, 2011, Aron Broom wrote:
>
> 2) I ran the water dimer test just using the oxygens for each water and the
> PMF is semi-reasonable, but the entire simulation suffers from the fact
> that the distance can become larger than the range I'm interested in.
You could use a "flat bottom" NMR-type constraint to keep the O=O distance
from getting too big, e.g.
&rst iat = 3,6, r1=0.1, r2=2.0, r3=12.0, r4=99.0, rk2 = 0.0, rk3=10.0, /
This (untested!) restraint will have no effect until the distance between
atoms 3 and 6 gets to 12 Ang, and then the energy will rise quickly, pushing
the two molecules back together.
....dac
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Received on Tue Dec 06 2011 - 18:00:03 PST
