[AMBER] GB and Dielectric constant

From: kanika sharma <ksharma997.gmail.com>
Date: Mon, 9 Apr 2012 17:19:29 +0530

 Dear All,

In AMBER, there are two methods to use implicit solvent. One is
(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 - 05:00:02 PDT
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