Re: QM/MM MD and the qmParamPDB file

From: Agisilaos Chantzis (
Date: Thu Aug 16 2018 - 04:25:56 CDT

Dear Marcelo,

thank you very much for the clarification. I will download the latest
nightly build for NAMD, since as you guessed I am using the 2.12 version.

By the way, I guess the utility of the qmParamPDB file is just to define
the QM and MM atoms and actually no coordinates are read from this file,
right? I am asking because I am using the same qmParamPDB file for all
MD jobs (e.g. minimization, annealing, equilibration etc) and it is
important to know that the actual atomic coordinates are being read from
the previous run to the actual run.

Thank you very much for your feedback!



On 16/08/18 04:43, Marcelo C. R. Melo wrote:
> Dear Agisilaos
> Internally, NAMD distributes atoms (both QM and MM) in "patches" that
> can change order and exchange atoms, so the order in which atoms are
> processed can change from step to step, without causing any problems.
> However, for people doing advanced processing of QM results, this
> could be an issue, so we changed this behavior to make sure that every
> QM input file (MOPAC, ORCA or using a custom script) would be the same
> throughout the simulation, and across simulations. This is implemented
> in the nightly build of NAMD. Is it possible you are using the version
> 2.12 of NAMD, or earlier?
> Best,
> Marcelo
> ---
> Marcelo Cardoso dos Reis Melo
> PhD Candidate
> Luthey-Schulten Group
> University of Illinois at Urbana-Champaign
> <>
> +1 (217) 244-5983
> On Wed, 15 Aug 2018 at 07:50, Agisilaos Chantzis
> < <>> wrote:
> Dear all,
> While running QM/MM+MD trajectories with NAMD and ORCA I have noticed
> that for each force calculation cycle the ordering of the QM atoms in
> the ORCA input file are changing. Although this seems not to alter
> the
> results (the molecule seems as it should be) I was wondering
> whether in
> a series of sequential QM/MM+MD jobs (e.g. minimization, annealing,
> equilibration etc) the PDB file specifying the QM atoms (the
> qmParamPDB
> file) should be the same in all configuration files or has to be
> changed
> to reflect the numbering of the QM atoms at the end of the
> previous run.
> I understand that for jobs without bonds being cut due to the QM/MM
> partition of the system this atoms reordering should not have any
> effect
> because the QM part will always remain the same, but what about the
> general case of cutting through bonds?
> Sincerely,
> Agisilaos

Dr. Agisilaos Chantzis, Ph.D.
Computational Quantum Chemist
338 City Road, London
United Kingdom

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