AMBER Archive (2008)

Subject: Re: AMBER: Minimisation and heating under GB conditions

From: Carlos Simmerling (
Date: Mon Nov 03 2008 - 05:29:25 CST

that seems extremely simplistic to me- I usually use a much more
complex equilibration protocol.
I also use a 1fs step during equil, and restraints that are turned off
slowly. I also use no cutoff in GB.
I find that heating starting at 0 can produce serious problems (you
are scaling V an infinite amount),
so I start at 100K and heat from there. that minimizes the effect of
any hot spots. use shake and either 1fs step or 1fs + respa.
if your structure came out ok then maybe this is fine, but things in
GB tend to be more sensitive to equil because of the lack of the
solvent cage keeping the initial structure.

also I STRONGLY recommend against igb=1. we've published several
papers (as have others) showing that this is not a good option. I
recommend igb=5 and mbondi2 radii.

On Mon, Nov 3, 2008 at 3:58 AM, Francesco Pietra <> wrote:
> Coming from experience with periodic boundary conditions, I started
> minimization and heating of a large protein-polypeptide complex under
> GB conditions, where I had no experience.Looking a posteriori to
> tutorials, I wonder whether the conditions I used allow continuing
> safely with MD.
> minin:
> mod21_polyp initial minimization prior to GB MD
> &cntrl
> imin=1,
> maxcyc=5000,
> ncyc=2500,
> ntb=0,
> igb=1,
> cut=12
> /
> heating:
> heating gradually under GB conditions
> &cntrl
> imin=0, irest=0, ntx=1, ntb=0,
> igb=1, ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> nstlim=25000, dt=0.002,
> tempi=0.0, temp0=300.0,
> cut=12
> /
> &wt TYPE='TEMP0', istep1=0, istep2=25000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
> I assumed that a cutoff of 12 would have been enough under GB
> conditions but I am now unsure given the size of the protein (ca
> 20,000 atoms in total plus the polypeptide). Also, was the cost on no
> SHAKE during heating worth while (and dt as large as 0.002 correct)?
> Carrying out analysis by Ross Walker's script proceed_mdout.perl,
> TEMP, EPTOT, EKTOT, and ETOT after heating are OK. Also, the initial
> and "heated" structures superimpose at the open eye and Multialign in
> Chimera is correct.
> Thanks for advice
> francesco pietra
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