On Fri, Aug 17, 2018, 龚乾坤 wrote:
>
> There are two modes (the NAB implementation of nmode is used or the
> "original" nmode implementation is used.) to calculate entropy in
> MM_PB/GBSA.
>
> I have used these methods to compute entropy, however, I find there is a
> huge difference between NAB_nmode and original nmode. So, I want to ask:
> First, why arise huge difference between them ? Second, I wang to know
> which is more accuracy about two modes.
My guess is that the NAB nmode calculation is using GB, whereas the
(very old) nmode code doesn't know anything about GB.
> # DIELC - (Distance-dependent) dielectric constant (if IGB = 0)
> can you explain the meaning about DIELC - (Distance-dependent)
> dielectric constant (if IGB = 0)? and why DIELC=4 ?
As the message above (tries to) indicate: DIELC is ignored unless IGB=0;
but you have IGB=1. So it doesn't matter what value for DIELC is
provided.
I'd recommend using gb and the NAB version of nmode: it should be more
correct, since it incorporates a notion of solvent screening via GB.
....dac
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Received on Fri Aug 17 2018 - 06:30:04 PDT
