Re: [AMBER-Developers] ifcap and GB - potential problem?

From: Ben Roberts <>
Date: Fri, 26 Mar 2010 19:21:24 -0400

Hi Dave,

On 26/3/2010, at 12:36 p.m., case wrote:

> generally speaking, my guess is that combining cap waters with GB has *only*
> ever been tested with the hybridgb flag turned on.
> I'd say we should require hybridgb to be turned on if both gb and ifcap are
> on; there is probably(?) no harm in reading the extra prmtop sections when
> ifcap is turned on. If we(you) added both changes, then users' who really
> wanted both ifcap and gb (but not in the context of hydbrid gb) could get
> that by a simple modification of the code, and we would still be protecting
> "young players" from using what are otherwise untested combinations.

Hmm. Now I get into muddy waters.

So we have:

ifcap=1, igb>0 = maybe OK, but untested. Considered dangerous.

ifcap=1, ipb>0 = ??? radii will not be read, but the manual seems to recommend
use of igb=10 with solvent caps. Is that dangerous, or are P-B parameters read
from elsewhere anyway?

ifcap=1, hybridgb>0 = tested to an extent? I tried to read the manual here, and
it didn't really explain the relationship between ifcap (as a setting in the
prmtop) and hybridgb. The manual suggests that what hybridgb is really for, is
the situation where waters beyond a certain distance away from the solute (but
determined by a number of waters to keep) are treated as a continuum. The example
(rem_hybrid) does not use ifcap.

Also, I'm trying to make sense of your suggestion. Do you suggest that I ask for
the sections to be read anyway, but put in a fatal error if ifcap=1 and igb>0,
so that experienced people can comment the error out and continue on their way,
but those less experienced get the message? That is, do both things I suggested?

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Received on Fri Mar 26 2010 - 16:30:03 PDT
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