Re: Reg: deciding cell basis vector

From: Aron Broom (
Date: Mon Jul 21 2014 - 12:39:39 CDT

Hi Akshay,

If you follow a reasonable strategy for choosing the basis vectors (like
just measuring the box dimensions in VMD) and then do say ~1 ns of
simulation with pressure control, you will almost certainly get something
that is appropriate. Generally the simulation will not crash unless you
make a very bad initial choice on the cell basis vectors.

For the PME, you can just set the PMEGridSize (I think that is the name of
the parameter) to 1.0 or 0.9 (those are reasonable values) and NAMD will
handle automatically setting the grid dimensions to be something
appropriate, so you needn't worry about optimizing things for factoring.

On Mon, Jul 21, 2014 at 9:57 AM, Akshay Bhatnagar <> wrote:

> Hello everyone
> I am having an amino acid for simulation in 20 angstrom water box. the
> system is at the origin.
> Can anyone tell me the criteria to decide the cell basis vector for x, y
> and z dimensions apart from what is there in the tutorial.
> Also, is it correct to say that PME should be the which can be factorize
> by 2,3 or 5 and the ratio of cell basis vector/PMEGridSize should be
> slightly less than 1 (around 0.9).
> Thanks
> With Regards
> Akshay Bhatnagar
> PhD Student
> BITS Pilani Hyderabad Campus

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:37 CST