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

From: Elvis Martis <>
Date: Sat, 4 Feb 2017 08:25:57 +0000

I don't think you can separate this way for memory intensive jobs and those which are not memory intensive in MMPBSA for single run.
However, I usually do my enthalpy calculations on all snapshots and entropy calculations on every 5th snapshot.
And, also perform enthalpy calculations separately and entropy calculations separately (MAX with 8 CPUs for 24 GB RAM).
    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Abhilash J []
Sent: Saturday, February 04, 2017 11:57 AM
To: AMBER Mailing List <>
Subject: [AMBER] Number of threads in MMGBSA/MMPBSA calculations.

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 more.
  This will save me and others like me days of calculation in some cases.


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