I agree that multiple trajectory methods such as REMD will help in
exploring the conformational changes and extract representative
ensembles at different temperatures. However, with a large system like
the one I am currently working on, where solvent molecules play an
important rule in bridging the interactions between the protein and
DNA, I think this my require a tremendous computational power.
In the meantime, the entropy dependance on temperature returns me to
the first square. That is, how to specify temperature in the mm-pbsa
input file?
Thanks for your help and the through explanation.
Khaled
On 20-Sep-10, at 8:22 PM, manoj singh wrote:
> Yes, I missed the two terms, the solute entropy and solvent entropy.
> It is
> certainly not a good practice to estimate the entropies at a diff
> temps with
> a traj created at some other temp. Provided simulation has been run
> "long
> enough", it should capture all relevant conformations with significant
> population at that temp, however, as mentioned, REMD can make life
> much
> easier.
>
> On Mon, Sep 20, 2010 at 10:04 PM, Thomas Cheatham <tec3.utah.edu>
> wrote:
>
>>
>>> I'm trying to run mm-pbsa at different temperatures to analyze the
>>> effects of temperature on the binding of a protein-DNA complex. I
>>> was
>>> wondering if there is a way to specify the running temperature as a
>>> parameter for the mm-pbsa script. I tried to set the temp variable
>>> to
>>> the desired temperature, but it seems there is no effect. I am using
>>> the mm-pbsa perl scripts with amber 10.
>>
>> No effect, seems correct to me. I would not expect much of an
>> effect in
>> mm-pbsa. Remember,
>>
>> deltaG = deltaH - T deltaS
>>
>> There is no temperature dependence to the "H" (loosely equivalent
>> to the
>> potential energy in the MD). Where temperature has an effect is in
>> the
>> entropy term which is solute entropy (via nmode or other estimates
>> which
>> may not even be turned on in your mm-pbsa analysis since it tends
>> to be
>> expensive) and potentially the solvation free energy term although
>> this is
>> likely small in a continuum approximation...
>>
>> It is highly unlikely you will be able to get temperature
>> dependence from
>> a single trajectory at 300K since at higher temperatures a larger
>> ensemble
>> of conformations would be sampled (meaning higher entropy and
>> sampling of
>> higher potential energy structures). To get the temperature
>> dependence,
>> likely a replica-exchange approach (at minimum) would be required...
>>
>> --tec3
>>
>>
>>
>>
>>
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Received on Mon Sep 20 2010 - 20:30:03 PDT
