Re: how should I set those PMEGridSizeX,Y,Z?

From: Tim Isgro (timisgro_at_ks.uiuc.edu)
Date: Thu Dec 11 2003 - 18:00:13 CST

YingXiong,

PMEGridSizeX,Y,Z sets the number of grid points, which always cover the
entire length of the cellBasisVector. Thus, if cellBasisVector1 = 100 and
PMEGridSizeX = 60, there would be grid points every 100/60 = 1.67 Angstrom
along the cellBasisVector1 direction.

Tim

On Thu, 11 Dec 2003, wrote:

> Dear Tim,
> Thank you for your explanation and direction!
> I can understand " the number of grid points", but I can't understand the
> meaning of "Grid size". Because PMEGridSizeX,Y,Z sets the number of grid points
> along cellBasisVector1,2,3 respectively, why can these points decide the size of
> grid? Maybe the distance between each point is fixed (for example, 1 angstrom ).
> That is to say, For a cellbasisvector of 100, the length of cellbasisvector1 is
> 100 angstrom, if PMEGridSizeX is 30, then the size of grid is 30 angstrom along
> cellBasisVector1, the grid only covers part of the cell. if PMEGridSizeX is 120,
> then the size of grid is 120 angstrom along cellBasisVector1, the grid covers more
> than all the cell.
> Is my understanding right?
>
> YingXiong
>
>
>
> >From: Tim Isgro <timisgro_at_ks.uiuc.edu>
> >Reply-To:
> >To: <yxiong_at_mail.ccnu.edu.cn>
> >Subject: Re: namd-l: how should I set those PMEGridSizeX,Y,Z?
> >
> >PMEGridSizeX,Y,Z sets the number of grid points along cellBasisVector1,2,3
> > respectively. The online NAMD manual says each should have small integer
> > factors (2, 3, and 5) for best running speed (but I have no idea why).
> > In choosing the grid size, you'll want to balance computational effort with
> > accurately representing the charge in your system.
> >
> > For a cellbasisvector of 100, a reasonable grid size could run from 30
> > (less accurate, but faster) to 90 or 120 (more points for charge, slower
> > running).
> >
> > -Tim
> >
> > On Wed, 10 Dec 2003, wrote:
> >
> > > Dear sir,
> > > When I use PME method in MD, how should I set those
> PMEGridSizeX,PMEGridSizeY,
> > > PMEGridSizeZ? Whether need these values be larger than cellBasisVector1,
> > > cellBasisVector2,cellBasisVector3 respectively ?
> > > I am looking forward to your help!
> > >
> > >
> >
> >
>
>

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