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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
