Re: parameters for GB use

From: David Case <>
Date: Fri 24 Nov 2000 10:02:57 -0800

On Fri, Nov 24, 2000, Mark Forster wrote:
> My question concerns the use of the Generalised Born (GB) solvation method.
> Since the PME method is "always on" in the AMBER6 version of Sander
> and PME is only intended for periodic system simulations,
> how are the non bonded terms now computed in the case of the a GB
> simulation in a non periodic system ?

setting igb>0 turns off PME.

> Does the code then utilise atom based cutoffs and does the 'CUT' parameter
> still control these terms ?

Yes. The manual seems clear (to me!) on this point. Note that for GB,
CUT should be set much larger than the default value of 8.0.

> Finally, is the default value of SCEE=1.2 the correct value for a GB study ?

SCEE is independent of whether you use GB or not. It should be set to 1.2
for the 1995 and later Amber force fields, and to 2.0 for the 1991 and
earlier Amber force fields.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Fri Nov 24 2000 - 10:02:57 PST
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