Dave - no I haven't tried that during equilibration, since tighter coupling
fixes it I just made it part of our equilibration protocol long ago and
moved on. I'll try that since I have a sample setup with a bubble and see
if it works better.
carlos
On Thu, Oct 22, 2020 at 8:48 AM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Oct 21, 2020, Carlos Simmerling wrote:
>
> >what is your pressure coupling constant? I often get vacuum bubbles unless
> >I include a step in my equilibration with tight coupling, taup around 0.1
> >or smaller.
>
> Carlos: have you ever tried barostat=2? It would be interesting to know
> if that makes a difference. Also, what is your starting density? If
> you use a closeness parameter of 0.7--0.8 (in solvateBox or solvateOct),
> you'll get a higher starting density, which might(?) reduce the tendency
> to get bubbles.
>
> ....dac
>
>
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Received on Thu Oct 22 2020 - 06:30:03 PDT
