On Mon, Jun 15, 2015 at 10:45 PM, Huang <huangloligo.gmail.com> wrote:
> Thanks for the reply.
>
> I used cut=22.0 for saving conputer time, while I forget if I read
> somewhere that cut=20.0 is used for such a simulation (and I choose a
> better one, like cut=22.0). Will this setting introduce manifacts?
>
>
Hard to tell. The issue is that electrostatic interactions are *very*
long-range. Have you compared the performance of using a 22 A cutoff
compared to a 1000 A cutoff? Unless the latter is prohibitively expensive,
using 1000 A is better for implicit solvent calculations.
> Jason said that "Seems like a good idea to me." I guess you didn't
> think it is necessary to keep using LCPO and surften=0.00500. Am I
> correct?
>
I honestly don't remember the original context. But given what I see
below, I said that it seemed like a good idea to keep using LCPO with a
surften of 0.005 in the MMPBSA.py run. But then Carlos pointed out that
you didn't set gbsa=1, which means that you didn't use LCPO in the original
calculation.
The default values for the non-polar solvation free energy with GB is
usually decent, so if you are unsure of what to do, that is a good starting
point.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 15 2015 - 23:00:02 PDT
