From: Ravinder Abrol (abrol_at_wag.caltech.edu)
Date: Fri Feb 24 2006 - 12:59:52 CST
The PDF link:
asks for a Document Open Password.
Do you know what that is?
On Fri, 24 Feb 2006, LEWYN LI wrote:
> 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:
> Hope this helps!
> 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
> > ---------------------------------
> > Yahoo! Mail
> > Use Photomail to share photos without annoying attachments.
-- ________________________________________________ Ravinder Abrol 139-74, Beckman Institute Division of Chemistry and Chemical Engineering Caltech, Pasadena, CA 91125 Phone: 1.626.395.8143 Fax: 1.626.585.0917 Email: abrol_at_wag.caltech.edu ________________________________________________
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