Many thanks Jason for the quick reply.
In answer to your question, I applied the restrains to the whole complex (all protein residues, water, ligand).
Looking at advanced tutorial 3 (
http://ambermd.org/tutorials/advanced/tutorial3/section1.htm), the authors applied restraint_wt = 2.0. Isn't this excessive? Is there a reason for applying such restraint?
My last question is whether there is a way to tell whether my observation is an imaging artifact or not?
Best regards
George
On Nov 13, 2013, at 10:18 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Nov 13, 2013 at 3:41 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Hi everybody,
>>
>> I'm simulating a system in which there is a conserved water molecule in
>> the binding site of the protein. I used restraint_wt=1.0 during energy
>> minimization, restraint_wt=0.1 during heating and density equilibration.
>> This resulted to the water molecule flying out of the binding site.
>>
>
> I wonder if this is an imaging artifact. These are actually fairly strong
> restraint weights for dynamics (assuming that r1 and r4 are significantly
> smaller and larger than r2 and r3, respectively). Even with a restraint
> weight of 0.1, there is about a 1 kcal/mol penalty for a single particle to
> move 3 Å away from the reference position.
>
> Are you applying the positional restraints to the whole system or just to
> the conserved water molecule?
>
>
> It's obvious that I should had used stronger restraints. Is there a rule of
>> thumb as to the range of restraints that one should use during
>> minimization, heating and density equilibration? Should there be a gradual
>> relaxation of restraints before production MD?
>>
>
> If you ultimately plan on getting rid of the restraints, then what you used
> is typical compared to what I use.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Nov 13 2013 - 16:30:02 PST
