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

[MPI]

Hi Max, Thanks for the paper. This is helpful. -Dewey

Ebert Maximilian wrote:
> Hi Dewey,
> maybe a little bit off topic but your description of the system reminded me of a paper I read a couple of years ago. Do you know about the ABF method and the work of Lamoureux et al? (http://pubs.acs.org/doi/abs/10.1021/ja300129x) maybe worth checking because it sounds like the simulation you want to execute (even though they don’t use GROMACS).
> Max
> On May 31, 2015, at 4:17 PM, MPI <mpi566 at gmail.com<mailto:mpi566 at gmail.com>> wrote:
> Dear Users,
>    I have a protein-lipid bilayer system and this protein is an ion
> channel.  I would like to force a substrate eg, ammonia (NH3) passing
> through this channel.
> 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
> Also,  if the substrate has a charge, which order is preferred ?
> Thanks,
> Dewey