Membrane protein simulaton

From: snoze pa (
Date: Fri Jan 14 2011 - 18:19:24 CST

Dear NAMD users,

I am trying to setup a NAMD simulation for membrane protein. I have a
question related to setup?

1. I have to remove part of the lipid that is in contact with protein.
I am not sure how much of the lapid molecule I should cut? shall I
remove with in 0.6A from protein?

2. How can I avoid water from entering into membrene during
simulation. I found a script keep_water_out.tcl in NAMD tutorial but I
don't know how to use it.

I will highly appreciate your help solving this protein.

Thanks in advance.


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