[gmx-users] Adding a substrate into protein-lipid bilayer system

[MPI]

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 ?