VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 07 2011 - 12:43:57 CST
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Hi,
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.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
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
>
>
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
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