Dear Prof Case,
Thanks for your helpful email. I have fixed the previous error (Although I
have not narrowed down the issue, using another MD configuration seemed to
have fixed this behavior).
I just have one more question regarding running TI on estimating relative
P-P binding free energy. Near small (ie. 0.00922) values of lambda (I'm
using a 12-point lambda transformation), there are geometries where the
almost "ghost"-like softcore atoms are sterically clashing and actually
goes through the rest of the protein, and give exceptionally high VDW
energies. I was just wondering if this behavior is normal in TI. Another
one of my concerns is that if I were to start the next lambda simulation
from the end of the current, clashing state, I am fearful that this would
lead the system to crash. Sorry for these naive questions, and thanks for
your time.
Best,
Wanlei
On Fri, Apr 9, 2021 at 8:12 AM David A Case <david.case.rutgers.edu> wrote:
> On Thu, Apr 08, 2021, WW wrote:
>
> >when trying to run TI, which is that the periodic
> >boundary conditions seem to "fall apart" and start to form a droplet after
> >heating during the equilibration phase of the simulation.
>
> It's a little hard to understand the problem here. Your sample input file
> is for constant volume. If your intial density is off, there might not be
> enough matter to fill the entire box, and you can get droplets.
>
> So, what is your density? It's not printed by default until you turn on
> constant pressure, but Parmed will report it with the "summary" action.
> Find out what happens when you go to the constant pressure stage.
>
> Please turn off iwrap=1, at least for debugging. This variable is only
> needed in exceptional cases, and itself can cause problems. Also, you
> should check if this problem has anything to do with TI by running a
> standard simulation to see what behavior you get.
>
> ...good luck....dac
>
>
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Received on Sat Apr 10 2021 - 20:00:02 PDT
