RE: Cell Basis Vector.

From: Pijush Ghosh (
Date: Wed Sep 08 2004 - 23:20:22 CDT

NAMD Friends,
    thank you all for your valuable suggestions. I am still not able to
solve my problem I addressed. I tried with changing the PME to >=BoxSize
and a multiple of 2,3 and 5 as suggested one friend but still its not
     The dimension I mentioned below is the overall dimension of my
model(i.e max. extension in X,Y and Z)and it is a montmorillonite clay
     Is anybody aware of any general relation between this
switch,cutoff,pairlistdist with cellBasisVectors?

     Your guidance and suggestion is highly appreciated.


Hie NAMD Friends
                I am recently facing a problem and is really troubling
      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

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.

Pijush Ghosh
PhD Student.
North Dakota State University.
Fargo. ND 58105.

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