From: Isaac Twelves (twelves_at_ualberta.ca)
Date: Fri Jul 07 2017 - 13:04:37 CDT
Dear NAMD users,
I am currently trying to perform cv-SMD simulations whereby I allow water
molecules to travel through the pores of the AqpZ tetramer. I have been
closely following the 'Membrane Proteins' and 'Methods for calculating
potential of mean force' tutorials, as well as the procedure described in:
https://www.ncbi.nlm.nih.gov/pubmed/16084383, and adapting them to my
system.
Starting with a well-equilibrated AqpZ-POPC bilayer system, I placed 4
individual water molecules 5 angstroms away from the top of each individual
monomer (at the cytoplasmic end) and developed 5 systems: one where each
water molecule was constrained seperately to its initial position and one
where every water molecule is constrained simultaneously. I did this
because I would like to get a free energy profile for each monomer as well
as a weighted profile for the whole tetramer. Each system was minimized for
5ps and equilibrated for 150ps in an NPT ensemble.
I then ran the cv-SMD simulations with a 1fs timestep, 156pN/A spring
constant and a 0.01A/ps pulling velocity, and in only one of the
simulations did water permeate completely through the channel. In the other
sims, the water molecules hang around the pore entrance and do not permeate
at all.
I realise there are many other details I am leaving out for the moment such
as how the
AqpZ tetramer was built, how it was embedded in the POPC bilayer,
subsequent minimizations/equilibrations, etc. that I would readily
elaborate on if needed. Also, I can attach all the relevant SMD files if
that would help diagnose the problem.
Thanks you very much in advance,
-- Isaac Twelves 4th year Co-op Student, Department of Chemical and Materials Engineering, University of Alberta
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