Re: Pressure related issue

From: Axel Kohlmeyer (
Date: Thu Oct 16 2008 - 09:16:02 CDT

On Wed, 15 Oct 2008, Anirban Ghosh wrote:

AG> I am trying to simulate a CG system using NAMD. I using implicit solvent
AG> condition along with Periodic Boundary Condition and Particle Mesh Ewald.
AG> However, when I am using a constant pressure condition (which is
AG> recommended for PBC), my simulation is getting stopped saying "Box size is
AG> too small". Bu on removing the constant pressure condition, the simulation
AG> is running fine.

AG> So is it good to run the simulation using PBC but without constant
AG> pressure condition?

please _think_ about what you are doing, and you will understand
that this must happen.

you are using an _implicit_ solvent, i.e. there are no real water
molecules, how should the box size matter for as long as it is large
enough to have no (significant) interactions between the periodic
images of your molecule(s)? with npt the box will, of course, shrink,
until the molecules repell each other, which is probably too small for
the given cutoff.


AG> Thanks.
AG> Regards,

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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