RE: QMMM Frequency Calculation

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Mar 21 2019 - 12:07:18 CDT

Kelly,
Sorry this is off list, but I was curious if I missed how you got orca parallelized over the 16 cores?
Brian

From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> On Behalf Of McGuire, Kelly
Sent: Thursday, March 21, 2019 9:55 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: QMMM Frequency Calculation

  With ORCA working in parallel on 16 processors now, my QMMM is going fast. But, if I add in frequency calculations, the QMMM simulations slows down, predictably. I don't necessarily need the thermochemistry for every step any way. So, my thought is watch the trajectory, and any steps where there is something "interesting" happening, such as a covalent bond forming, save the frame before the bond formation as a PDB and the frame where the bond has formed as a PDB, and then run a frequency calculation on those frames/structures, I guess holding the MM region frozen, and that would give me thermochemistry data for the important parts of my QMMM. What are your thoughts on this?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

This archive was generated by hypermail 2.1.6 : Thu Sep 19 2019 - 23:20:25 CDT