Re: polymerization simulations

From: Giacomo Fiorin (
Date: Thu Jul 09 2015 - 15:51:38 CDT

Hello Luca, if you're referring to QM/MM support, it may be a good idea to
think first about the quantum mechanical method that you want to use (DFT,
MP2 or other post-HF methods) since these are the major constraint when
considering the coupling between quantum and classical MD.

What does the quantum chemistry literature say for the proteins of your


On Thu, Jul 9, 2015 at 2:06 PM, L. Signorile <>

> Hi,
> I have used NAMD for some time now but just for "basic" MD simulations
> (NVT/NPT, no harmonic restraints, constant temperature, PBC). I have a
> general question and I apologize if it is naive. I was wondering if it is
> possible to simulate the polymerization of protein subunits (like actin or
> tubulin) with the accompanying nucleotide hydrolysis. Is there any way to
> combine a "Monte Carlo-like" approach and a quantum mechanics approach with
> classical MD using NAMD?
> Thanks in advance,
> Luca

Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213

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