Re: applying constant force on water molecules in a particular direction

From: Giacomo Fiorin (
Date: Wed Sep 06 2017 - 07:08:34 CDT

Only a few basic features are covered in the NAMD *tutorial*.

You want to choose one of many options to apply external, user-defined
forces, all of which are covered extensively in the NAMD *manual*:

On Wed, Sep 6, 2017 at 7:14 AM, Sanjib Paul <> wrote:

> Dear Namd users,
> I have a system where two water baths are
> connected through a single walled carbon nanotube. I want to apply a
> constant force on all water molecules of these two baths along a particular
> direction (say +z or -z direction). The water molecules inside the nanotube
> will not experience any external force. Few research groups have done these
> type of simulation using steered molecular
> dynamics (Zhu *et al*. Biophysical Journal, *83*, *2002*, 154 –160). I
> have gone through the NAMD tutorial but what I am trying to do is quite
> different from the content kept in tutorial. So can anyone please show me a
> way to do this?
> Thanking you.
> Sanjib Paul
> Department of Chemistry
> Indian Institute of Technology, Kharagpur
> India

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

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