Re: AMBER: Minimisation and heating under GB conditions

From: Francesco Pietra <>
Date: Mon, 3 Nov 2008 15:08:42 +0100

On Mon, Nov 3, 2008 at 12:29 PM, Carlos Simmerling
<> wrote:
> 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.

On the basis of your kind comments above and below, I decided to
restart from scratch.

As I used

model3 = combine {model1 model2}

saveamberparm model3 xxxx.prmtop xxxx.inpcrd

where to set the command (or where is it described) "set default
PBradii bondi mbondi2" on the last line above?

>I also use no cutoff in GB.

I assume that means "cut=999"


> 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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Received on Fri Dec 05 2008 - 10:30:51 PST
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