Dear prof. Case,
thank you for your comments.
Best wishes,
Marek
Dne Mon, 31 Jan 2011 03:11:57 +0100 case <case.biomaps.rutgers.edu>
napsal/-a:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> __________ Informace od ESET NOD32 Antivirus, verze databaze 5832
> (20110130) __________
>
> Tuto zpravu proveril ESET NOD32 Antivirus.
>
> http://www.eset.cz
>
>
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 31 2011 - 02:30:02 PST
