[gmx-users] Adding a substrate into protein-lipid bilayer system
Justin Lemkul
jalemkul at vt.edu
Mon Jun 1 13:41:21 CEST 2015
On 5/31/15 4:17 PM, MPI 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
>
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.
>
> Also, if the substrate has a charge, which order is preferred ?
>
Charge shouldn't affect the protocol.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
More information about the gromacs.org_gmx-users
mailing list