Membrane Simulations

From: Anshu Bhatia (ciphurus_at_gmail.com)
Date: Wed Oct 22 2008 - 20:04:38 CDT

Hi,
I asked this question on the forum before but did not get a satisfactory
response so far. Let me try and rephrase my question.

I am trying to study the spatial variation in lipid bilayer properties due
to the presence of a gramicidin channel in the middle of the bilayer.
Because a gramicidin channel is smaller in length than the lipid bilayer
thickness, I expect the bilayer to shrink near the channel, but retain
its normal thickness far away from the channel.

I need help in developing a protocol for my specific problem. From the
protocols I have seen so far, I have 2 questions for the protocol:

(1) All protocols seem to constrain the head groups of lipids for a short
period of the time and let the lipid tails melt before letting the whole
system evolve.
 This melting is done to interlace the lipid chains without changing the
thickness. In some protocols this melting is done in NVT ensemble.
What is the reason to choose NVT over NPT?

(2) After this melting is performed most protocols use an NPT ensemble with
constant area or constant ratio for production runs.
Why is constant area used? In my case, I am interested in looking at the
variation in properties of lipid across the space, should constant ratio
still be used.

P.S.: If anyone can provide me with a good reference paper which discusses
issues about lipid simulations in namd, I would be very thankful

Anshu.

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