Re: Layers

From: LEWYN LI (
Date: Tue Nov 16 2004 - 13:38:13 CST


         I am not sure exactly what you mean, but here are a couple of

1. In the configuration file, you could specify all the atoms you would
like to "fix" i.e. hold constant in space. It requires that you put a
"1.00" in the B- or O-column in the pdb. For more info, you could just
google "fixedatom NAMD".

2. Why would you like to simulate with only two layers of water? My
understanding is that a protein simulation should have at least 3-5 water
layers around it to ensure proper electrostatic shielding and water
dynamics, especially if you use periodic boundary conditions.

3. The tutorials at the NAMD website is a great resource for how to
perform a simulation. The URL is:

         Hope this helps. Good luck!


On Tue, 16 Nov 2004, Laura De Luca wrote:

> Hi all,
> I'm a new user of NAMD.
> I would like to perform a molecular dynamic simulation of a big system which
> is solvate with two water layers, one inner layer and an outer layer.
> I would like to fix the outer (static) water layer which serves as solvent
> boundary.
> Could you please suggest me some papers/reviews that describe in detail MD
> simulations using this approach, i.e. the two water layers?
> Thanks
> Laura
> ---------------------------------------------------
> Laura De Luca, Ph.D.
> Dipartimento Farmaco-Chimico
> Universita'degli Studi di Messina
> Viale Annunziata 98168 MESSINA ITALY
> Phone: +39 090 6766464
> Fax: +39 090 355613
> email:

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