From: LEWYN LI (ll2150_at_columbia.edu)
Date: Fri Feb 24 2006 - 10:57:10 CST
Lily,
Accordingly to my experience, you need to both minimize and
equilibrate the system before running a NAMD simulation. The temperature
of the system after a minimization is zero. So, if you just run a
simulation of a zero-temperature system at any finite temperature, the
system may become unstable. I suspect this is why you got the "Atom
moving too fast" error message.
To equilibrate a system after minimization, you should gradually
heat the system up to the desired temperature, sometimes fixing certain
atoms or imposing so-called "harmonic constraints" on the system. It is a
bit of an art. I suggest that you consult the following and other
resources about equilibration:
www.orgitecture.com/folding/usr_doc/PracticalMD.pdf
Hope this helps!
LEWYN
On Thu, 23 Feb 2006, lily jin wrote:
> I am a new user a NAMD. Here is my problem:
>
> I tried to do only energy minimization with NAMD. So I let it do
> minimization for 500000 timesteps. Then I let it run 1 step (or 10
> steps). I was done with this start run. Then I tried to test if I can
> restart from step 500000, but I keep having the problem of "Atom moving
> too fast; simulation has become unstable" in my restart run.
>
> So I submit another job, where I let the minization go 500000 steps
> and then run 1000000 step. It run well. As it went to step 587000, I
> stopped it. After I made a restart file from step 587000. This time the
> restart run worked!
>
> So how can I only do energy minimization with NAMD? How can I restart
> from the last step of minimization?
>
> thank you!
>
>
>
>
> Lily
>
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