AMBER Archive (2004)


From: Ray Luo (
Date: Mon May 17 2004 - 16:43:55 CDT

Andreas Svrcek-Seiler wrote:

>>Could anybody tell me a good reference or an idea for a protocol to deal
>>with caps of water and Poisson-Boltzmann ?
>>My basic cuestion is how should I minimize the solvated complex before
>>molecular dynamics.
>>Is it better to freeze solute and minimize water separately or should I
>>directly minimize the entire complex?
>...What follows is based on experience with (dubious :-) droplet
>simulations without external dielectric continuum, but should also work here:
>1) Freeze (constrain) the solute and minimze the solvent a little bit (too
>much minimization leads to some "super frozen" lump of "ice", which
>takes *quite* a while to equilibrate again at e.g. room temperature).
>2) Do some equilibration-MD with the solute still constrained.
> It seemed ok to wait until E_VdW and E_Coul both fluctuate
> about constant average values.
>3) Equilibrate everything without constraints (except those you might want
>to keep).
>4) Do the production run (e.g. NVE - if the PB-procedure conserves
>total energy well enough).
In our previous tests, we simply minimize in steepest descent up to 500
step to relieve possible clashes (you don't have to use pb in the
minimization). Then heat it up slowly to target temperature using a
tight coupling constant. Finally perform the equilibration and
production run in constant temperature.

Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
Home page:

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