AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Nov 03 2008 - 08:45:22 CST

On Mon, Nov 3, 2008 at 10:08 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> On Mon, Nov 3, 2008 at 12:29 PM, Carlos Simmerling
> <carlos.simmerling_at_gmail.com> 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?
>
>
set PBradii should be set before you saveamberparm.

>>I also use no cutoff in GB.
>
> I assume that means "cut=999"
>

yes something larger than your system size.

> Thanks
> francesco
>
>> 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 <chiendarret_at_gmail.com> 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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