Thank you for your reply dac.
I read the description but this wasn't totally clear to me to be honest. So
just to be save: Re-run the simulation with default dielectric constant and
then changing it during mmpbsa/gbsa calculation?
-----Ursprüngliche Nachricht-----
Von: case [mailto:case.biomaps.rutgers.edu]
Gesendet: Montag, 30. Mai 2011 15:08
An: AMBER Mailing List
Betreff: Re: [AMBER] problem with dielectric constant
On Mon, May 30, 2011, Bernhard Poll wrote:
>
> I just wanted to do some mmpbsa/gbsa calculations with different
dielectric
> constants. So I added the dielc= command in the &cntrl section of my input
Did you read the description of this variable that says: "Please note this
is NOT related to the dielectric constants for generalized Born
simulations"?
We should add that it is NOT related to the dielectric constant for PB
simulations either. I'll update the manual to make the warnings more
explicit.
> So do I really have to re-run everything or do I only
> have to change the dielectric constant in the mmpbsa/gbsa sections?
You do need to re-run your simulations with the correct dielectric
parameters, then run the mm-pbsa analysis on those new trajectories. As you
have found, changing the dielc value just messes everything up.
....dac
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Received on Mon May 30 2011 - 07:30:03 PDT
