From: John Stone (
Date: Mon Nov 07 2011 - 12:43:57 CST

  Questions about the minutiae of NAMD simulations are best asked on the
NAMD list. It sounds to me like your timestep is far far too long.
A normal NAMD timestep would be 1fs or 2fs.

  John Stone

On Sun, Nov 06, 2011 at 07:04:39PM +0330, sarah k wrote:
> Dear all,
> I*m 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 atoms* 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

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