Hi Justin,
Thank you very much for your suggestion. Please see below.
Thanks,
Dewey
>> I wonder when it is appropriate to add NH3 into the system and how to
>> setup the control of temperature coupling in thermostats.
>> For example,
>>
>> 1. add NH3 first with the protein and then embed protein-NH3 into the
>> lipid
>> or
>> 2. embed the protein into lipid with an equilibration, followed by
>> adding NH3 into the system
>If you want NH3 to pass through the channel, I'd say (2), more or less, but
>really you should add NH3 as a cosolvent as part of the equilibration. Add the
>NH3 in the box, add water, and equilibrate.
If choosing (2), what is the concern ?
Why adding NH3 as part of water_and_ions after protein-lipid is
equilibrated already ?
Choosing (2), I have to go through equilibration twice.
Also, if the substrate is a very small ligand, is the protocol the
same ? Namely, adding a new substrate AFTER protein-lipid is
equilibrated. Then perform another equilibration for the substrate +
protein-lipid.
>> Also, if the substrate has a charge, which order is preferred ?
>Charge shouldn't affect the protocol.
Did you mean when adding a new substrate, eg, NH4+ or Ca2+ into a
protein-lipid system, one has to remove all ions and water in the
equilibrated protein-lipid system, put back ions and water again and
finally equilibrate the new system right after ?
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