From: sarah k (dailycolors_at_gmail.com)
Date: Sun Nov 06 2011 - 09:34:39 CST

Dear all,

Iím using NAMD to simulate a protein with multiple chains with 3100 atoms.
First I would run my simulation with timestep of 50 fs and cutoff distance
of 10. My simulation stops after about 20 million steps with the error that
some atomsí velocities exceed the limit. The structure does not break down.
I reduced the cutoff distance to 8. The program stopped with a blank *.out
file. Now,

1- What can be the root of problem?

2- I have to run a quick simulation. How many femtoseconds is the best
time step?

Best regards,

Sarah Keshavarz