Dear Professor Case,
first of all thank you very much for prompt answer !
Unfortunately it seems that regarding DIELC param. there
was some misunderstanding as I was talking about DIELC
parameter from the .NM section ((Distance-dependent) dielectric constant
with default value 4) and
your reaction was evidently focused on DIELC param. from .MM section where
it has different
meaning (Dielectricity constant for electrostatic interactions. with
default value 1)
So could you say some recommendation about the DIELC parm. from .NM
section regarding normal mode analyses in vacuum ?
#1
Say leave it on it's default value 4 (because it is related just to some
internal dielectric properties
of molecule (probably optimized for proteins) and not to solvent
dielectric effect )
#2
Change it on some different value (which) ?
#3
Do not use this approach and try rather experiment with small values of
EXTDIEL (in case PROC=1, GB=1 in .NM section) however
with great caution ...
You also mentioned that "the potentials were parameterized for condensed
phase simulations, and often do a very poor
job of representing what would really happen in vacuum"
You are speaking here (i) about shape of mathematic ff formula (too simple
for vacuum calc. ?) or (ii) about some ff parameters (bond, nonbond)
"optimization"
respect to condensed phase ?
In case of (ii) which ff parameters were optimized for condensed phase
simulations ? Could you recommend some article/s where
is this optimization described ? How it is with reliability of
"Calculation of gas phase energies" in MM/PBSA if
vacuum calculations with amber ffs is disputable ? Or "gas phase" doesn't
mean here "in vacuum" ?
Thank you a lot in advance for your additional comments !
Best wishes,
Marek
Dne Thu, 23 Jun 2011 18:13:51 +0200 David A Case
<case.biomaps.rutgers.edu> napsal/-a:
> On Thu, Jun 23, 2011, Marek Maly wrote:
>
>> > I want to do normal analyses of vacuum conformations of the given
>> > molecule.
>
> Then set igb=0 and don't change DIELC from its default value.
>
> (The only real use I know of for setting is DIELC to something other
> than 1 is
> for calculations that use a distance dependent dielectric, where epsilon
> = 4r.
> This was popular a long time ago (before the development of GB and other
> implicit solvent models), but never had much to recommend it.)
>
> Amber, and other simulation packages, indeed offer lots of options, but
> that often just gives users enough rope to hang themselves. As an
> example:
> you can say "I want to d normal [mode] analysis in vacuum...", and
> apparently do that. But you should remember that the potentials were
> parameterized for condensed phase simulations, and often do a very poor
> job of representing what would really happen in vacuum. So the code's
> ability to (apparently) carry out a vacuum simulation should be treated
> with appropriate caution.
>
> In general, changing parameters a long way from their default values,
> (such as
> changing EXTDIEL in gb to 1 from its default value of 78) is dangerous.
> Experimentation is instructive (and encouraged!), but please remember
> that the
> range of validity of simple force field models is limited.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
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 Thu Jun 23 2011 - 14:30:03 PDT
