Re: building system with or without water for metadynamics

From: Giacomo Fiorin (
Date: Tue Oct 17 2017 - 21:34:55 CDT

Dear Rabeta, you can also use metadynamics on examples that use ABF.
Metadynamics has fewer restrictions and will work on the same variables
that ABF does.

The tutorial you are referring to has a tiny system because it involves a
2D calculation, which takes a bit long for tutorial purposes. It is also a
conversion of the basic PLUMED tutorial, so it has mostly the value of
illustrating how to migrate between metadynamics implementations.


On Tue, Oct 17, 2017 at 8:06 PM, Vermaas, Joshua <>

> Tutorials tend to be aimed at being run with modest hardware
> requirements. This is why water was likely excluded, as it greatly
> reduces the atom count and lets the user see the evolution within the
> simulation without a supercomputer getting involved. Do whatever is most
> appropriate for your system.
> -Josh
> On 10/17/2017 03:57 PM, Rabeta Yeasmin wrote:
> > Dear NAMD users,
> >
> > I am trying to run meta-dynamics to find binding sites between a
> > protein and a ligand. I am wondering if I should include water in the
> > system. In the NAMD metadynamics tutorial files, there was no water in
> > the system. That's why I am confused if I should build the system with
> > or without water.
> >
> > Thanks very much.
> >
> > Rabeta Yeasmin

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

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