AMBER Archive (2006)

Subject: Re: AMBER: Restart problem on PMEMD with position restraint.

From: David A. Case (
Date: Mon Sep 18 2006 - 14:09:46 CDT

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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