[AMBER] Is it possible to run QM/MM-PIMD simulations with sander?

From: proszx <proszx.163.com>
Date: Wed, 16 Sep 2020 17:10:52 +0800 (GMT+08:00)

  I am using AMBER to simulate some large systems with a small active center. I use QM/MM descriptions and would like to use the PI representation for the atoms.
 I learned from the tests in AMBER/test that part-PIMD could only be run with sander.LES, while sander and sander.MPI support full-PIMD simulations. I do not need full PIMD here, but only a subset of the system (e.g. some hydrogen atoms in the active site) are represented with the beads representation. Therefore, I think I should used sander.LES and its MPI version.
  In my test, I find that the LES module does not support ifqnt>1, i.e. QM/MM simulations. Surprisingly, in another folder named pimd_pme in AMBER/test, there is a program named sander.PIMD, which could be used with some QM/MM potentials (PM3 if I recall). However, in the current version, there is not such sander.PIMD program.
  Can you give me some hints/tutorials about running PIMD with QM/MM potentials?
  Thank you in advance for you help.



Zhaoxi Sun


College of Chemistry and Molecular Engineering

Peking University
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Received on Wed Sep 16 2020 - 02:30:03 PDT
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