On Sun, Jan 30, 2011, Marek Maly wrote:
>
> My particular question is: Are there any recommendations regarding the
> value of IGB parameter in Normal Mode analysis section of
> input file for mm_pbsa.pl analysis ? I mean, it is better (to obtain more
> reliable results) to use GB model (IGB=1) or a
> distance-dependent dielectric (IGB=0) here if one would like to obtain TdS
> contribution of receptor/ligand complexation
> simulated in explicit TIP3P water ?
One quasi-ojbective answer is that the minimum point with gb is
generally (always in my limited experience, you can check for yourself
on your system) closer to the snapshot geometry you started from that
is something using igb=0. So, arguably, the properties of such a
minimum might be a better reflection of what is going on in the solvated
simulation.
A second point is that MD simulations using gb are generally (always?) more
faithful to the solvated dynamics than are MD simulations using igb=0. Again,
you could check this on your system.
Since the target configurational entropies are unknown, I don't know of any
direct way to establish the superiority of igb=1.
...dac
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Received on Sun Jan 30 2011 - 18:30:04 PST
