Thank you all for reply!
Now I think the problem is that I used the minimized structure as the
reference in my both NPT runs. In fact, I encountered this problem
before, and I dealt with it in this way: in the second NPT run, I use
the same reference, but with smaller restraint factor, and if needed,
shorter time step, 0.001. Then, after 200ps or more, the structure was
as if "pulled" back to the reference. Usually in the third NPT run, I
can use dt = 0.002 and a larger factor without Vlimit error. But I am
not sure this is correct. What's your opinion?
Chunhu
-----邮件原件-----
发件人: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] 代表
David A. Case
发送时间: Monday, September 18, 2006 12:10 PM
收件人: amber.scripps.edu
主题: Re: AMBER: Restart problem on PMEMD with position restraint.
On Mon, Sep 18, 2006, Chunhu Tan wrote:
>
> I got a Vlimit error when I wanted to restart a PMEMD simulation
with
> position restraint. My system is protein G solvated in a TIP3P water
box
> with 11 angstroms buffer. After the minimization, I first run 20ps NVT
> simulation, then 20ps NPT simulation. All these were OK, but when I
> wanted to restart the NPT simulation, I got the Vlimit error, even I
> used exact the same input file as the first NPT run.
What are you using as REFC for the run that failed? This must be the
restrt
file from the previous NPT run, *not* just the crystal structure (or
whatever)
coordinates. The reason is that the first NPT run scales the
coordinates,
but not the reference coords. So, when you start the second NPT run,
you
need to reference to scaled coords.
This is a (minor?) limitation of the Amber equilibration scheme. You
might
get around it by reducing the strength of your restraints by a factor of
10
or 50 (i.e. to use a restraint weight of 1-5 kcal/mol-A**2). A value of
50 is way too high in any event.
...hope this helps...dac
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Received on Wed Sep 20 2006 - 06:07:13 PDT
