From: Pijush Ghosh (pijush.ghosh_at_ndsu.nodak.edu)
Date: Tue Sep 07 2004 - 18:28:46 CDT
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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