Re: Question about QMMM simulation

From: Giacomo Fiorin (
Date: Sun May 31 2020 - 11:02:50 CDT

Hi Maryam,

On Sun, May 31, 2020 at 7:33 AM M. A <> wrote:

> Dear all,
> I am trying to run QMMM simulation without use of QWiKMD and I am doing it
> just with config files like the MD simulation.

That's actually how most simulations are run. QwikMD "flattens the
learning curve" for scientists new to MD simulation, but eventually you are
supposed to read the user's guide, starting from the parts that you are
interested in. The right place to begin is reading up on the subject
introduced by the "Info" buttons of QwikMD, which I hope is what you are

> I have a question about version of NAMD for running QMMM simulation. can
> we use NAMD_2.12_Linux-x86_64-multicore for this aim? or we should use the
> newer version of NAMD? I mention it again that I dont use QWiKMD plugin.

Both versions 2.13 and 2.14b1 contain several improvements to QM/MM
and in general it is always better to use a newer version, because there
are usually improvements across the board that affect all use cases.


> best regards
> --
> Maryam Atabay
> Ph.D in Nano Computational Chemistry
> Department of Physics, Sharif University of Technology

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD

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