Re: [AMBER] GB and Dielectric constant

From: Carlos Simmerling <>
Date: Mon, 9 Apr 2012 08:04:42 -0400

The distant dependent electric model is quite old and not a very good model
for solvation. You really should be using something like GB unless you have
a very good reason not to do so.
On Apr 9, 2012 6:50 AM, "kanika sharma" <> wrote:

> Dear All,
> In AMBER, there are two methods to use implicit solvent. One is
> Generalized-Born
> (GB) model , and the other is to use distance-dependent dielectric model. I
> have a confusion regarding distance-dependent dielectric model. If I want
> to see the solvent effect on protein, i should use this method ( eedmeth=5
> and diel = 4)
> So to run my simulation i used igb = 0 and ntb = 0 (non periodic). Does
> this mean that my simulation is in vacuum? I think it is so. But then how
> can the result be appropriate so as to check the effect of solvent on
> protein if it is run in vacuum, I mean it will not be correct. And turning
> igb = 1 will not let diel = 4 run simultaneously.
> I really want to know that using igb=0,ntb=o and diel=4, eemeth=5 the
> simulation result will be correct since it is run in vacuum.
> Secondly, what will be a simulation in implicit solvent.
> I donot know my questions seems logical or I could put my query well
> enough.
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Received on Mon Apr 09 2012 - 05:30:04 PDT
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