[AMBER] Number of threads in MMGBSA/MMPBSA calculations.

From: Abhilash J <md.scfbio.gmail.com>
Date: Sat, 4 Feb 2017 11:57:05 +0530

Hi everyone,

   I have observed that enthalpy calculation is not RAM intensive and
entropy is RAM intensive. When we run a job with both entropy and enthalpy
calculations, number of threads is dictated by the entropy calculations (as
RAM of a system is constant. 64 GB in my case) but the time is decided
primarily by entropy calculations as they tend to slow down due to less
threads. If you increase the threads enthalpy calculation will be fast but
entropy calculations will fail due to insufficient RAM. Hence there is
under utilization of the system. The problem is acute where the
trajectories are large 250ns or more.
  My question is, is it some how possible to separate the number of
threads in entropy and enthalpy calculations.
  I find that for long simulations this can lead to difference of a day or
  This will save me and others like me days of calculation in some cases.


AMBER mailing list
Received on Fri Feb 03 2017 - 22:30:03 PST
Custom Search