On Mon, May 12, 2003, Karl N. Kirschner wrote:
> The second simulation is one that has a cutoff = 0.0 in
> order to calculate the contribution of internal
> residue based EEL and VDWAALS energies.
Fox and Kollman used an earlier version of Amber that incorporated
residue-based cutoffs, in order to estimate the contributions of the
intra-residue nonbonded terms. [Even then, I doubt that they really ran
constant pressure simulations with zero cutoff, since those would quickly lead
to nonsense.] Anyway, residue-based cutoffs are no longer supported. If
you can find an old version of sander_classic, you could try your calculation
there. Otherwise, I think you will have to modify the code to compute the
intra-residue non-bonded interactions.
...good luck...dac
--
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David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
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La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Tue May 13 2003 - 16:53:00 PDT
