Re: [AMBER] Equilibration problem large system in explicit solvent

From: Jason Swails <>
Date: Wed, 7 Jan 2015 09:20:24 -0500

On Wed, Jan 7, 2015 at 8:12 AM, Waldner, Birgit <>

> Dear Amber users,
> I am trying to simulate a rather large system (tetramer) in explicit
> solvent (TIP3P 12Å octahedral box) using pmemd.cuda.
> After minimization, in my first NVT-equilibration step I keep the solute
> fixed (restraint_wt=1000.0) and slowly heat the system up from 100 to 300K.
> However, after this step, the equilibration crashes giving only the
> following error message:

​This restraint force constant is 2 to 3 orders of magnitude too large. It
is about twice the strength of the strongest bonds in the system and likely
introduces very high frequency vibrations that results in integration
errors blowing up your system (assuming your time step is the typical 0.002
or 0.001 ps). Consider using a restraint weight ~2 to 3 orders of
magnitude smaller (e.g., between 1 and 10).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 07 2015 - 06:30:03 PST
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