AMBER Archive (2004)

Subject: Re: AMBER: CAP PROTOCOL SIMULATION

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Tue May 18 2004 - 07:13:56 CDT

Hi,
> 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).
 
The optimal number of minimization/time steps might need some
experimentation, but the general procedure worked for me.

good luck
Andreas 

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                       svrci_at_tbi.univie.ac.at
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