SMD atoms not read properly!

From: Vani Krishna (
Date: Tue Aug 10 2004 - 07:49:42 CDT

Hello all:

Iam new to the SMD in NAMD and i have been having some
trouble with the SMD file. I have given a non-zero
value to 'N' number of atoms in my file, but when i
start the simulation, i see that in the log file, the
number of atoms regarded as SMD atoms are 'N-1'. The
program crashes immediatly as 'N' atom is connected to
'1', and Rattle tolerance is voilated. Can anybody
help me with this issue?

And also what is the good estimate for the 'K' value
to be given in SMD simulations?


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