Dear Christopher,
Thanks for your kind reply. :-)
Sincerely,
Shima
________________________________
From: Christopher Neale <[email protected]>
To: "[email protected]" <[email protected]>
Sent: Saturday, May 19, 2012 6:19 AM
Subject: [gmx-users] forcefields for lipids
Dear Shima:
I don't believe that anybody knows what lipid forcefield is best for the study
of ion conduction through a membrane channel, or if it even matters. My
instinct is that, for the timescales that you are likely going to use, the
particular lipid forcefield that you select is not going to make a
statistically significant difference, at least not any more significant than
your selection of cutoffs, ion concentration, decision whether or not to apply
dispersion correction, etc. That said, you certainly need a setup in which your
ion channel is stable. That is where I would start. Find some studies where
people have done something similar to what you want to do (if your channel is
alpha helical, then focus on channels like that) and try that forcefield
combination first. Before moving to umbrella sampling, check the overall
stability of your system by looking at backbone RMSD and perhaps using a
program like HOLE2 to ensure that the channel remains open
throughout the simulation.
Chris.
-- original message --
Thanks for all your suggestions.
Honestly, I want to simulate a protein-membrane system. My chosen membrane is
POPC. After the simulation of the system, I'm gonna apply the umbrella sampling
on the system to study the ion conduction through the channel composed of this
protein.
Before this, I had seen that the ion conduction through the gramicidin A
channel in a bilayer were studied using CHARMM. Refer to that article I guess
the CHARMM may give me the best out put. Is this an acceptable choice of a
force field?
Sincerely,
Shima
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