Re: Cell Basis Vector.

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Tue Sep 07 2004 - 18:45:13 CDT

Hi Pijush,

  I am confused by your email is the dimensions 32 X 27 X 29 (in A) the
size of the 'solute', or the min/max of the entire system (solute +
solvent)?

Ed

On Tue, 7 Sep 2004, Pijush Ghosh wrote:

> Hie NAMD Friends
>
> I am recently facing a problem and is really troubling me.
>
> The size of my model is 32 X 27 X 29 (in A). The part of my
> configuration file goes like this:
>
> switching on
> switchdist 12.00
> cutoff 15.00
> pairlistdist 16.00
>
> cellBasisVector1 40 0 0
> cellBasisVector2 0 40 0
> cellBasisVector3 0 0 40
>
> #PM
> PME on
> PMEGridSizeX 40
> PMEGridSizeY 40
> PMEGridSizeZ 40
>
> I am runing MD in NPT condition. With the above details i found the
> simulation is not running and ending up with 99999999999 and nan etc...I
> tried with other values of cell basis vector also. Similar type of
> problem i encountered earlier also but that time i played with some
> combination of switchdist and cell basis vector and found working but
> really couldnot make out what the actual rule is in NAMD.
> Can anybody help me in this matter and suggest me what is going to be
> the right combination for my system, or how i should proceed.
>
> Regards.
> Pijush Ghosh
> PhD Student.
> North Dakota State University.
> Fargo. ND 58105.
> USA.
>
>
>
>
>
>
>

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