[AMBER] Help with PB simulations using MPI

From: Jake <jezerski.central.uh.edu>
Date: Thu, 18 May 2017 14:34:54 -0500


I am trying to simulate a small 20 residue all atom peptide in implicit
solvent with a salt concentration of 150mM (saltcon=0.15). I have performed
these simulations using Generalized Born model and GBSA without any
problems in sander.MPI. I am now trying to use the same model with
Poisson-Boltzmann numerical calculations instead to improve my accuracy
(igb=10), but I get the following error message:

"PBSA currently doesn't work with MPI inside SANDER"

In my script I do not specify anything about surface area calculations. The
simulation works if I run non MPI sander, but it is significantly slower
and I will not be able to complete my simulations.

Is there any way around this bug? Can I use GBSA or some approximation for
the surface area terms and PB numerical calculations for the electrostatics?

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Received on Thu May 18 2017 - 13:00:03 PDT
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