Dear Albert, Pai-chi, Wen-qi, Jessica

Thank you for the draft of your sub-project requirements report.
My suggestions are below. Please incorporate them into your revision, adding
details of the substeps.
Please email Samrat and I, by Tue eve (at the latest).  We shall collect the
individual sub-group reports, link them on the web, and then discuss them in
class on Wed, and establish interdependencies between the groups.

Id like your group to compute the volumetric properties for the combined NMJ
domain (pre-synaptic membrane, postsynaptic membrane, AChR and AChE molecule
clusters, enclosed within a bounding rectangular gridded box).
(a) electric charge density
(b) hydrophobicity
(c) electrostatics potential

These volumetric properties need to be computed for two different states
(i) before activation of AChR-channels
(ii) after depolarization of post-synaptic membrane (post ion-permeation)

Property (a) should use atomic (quasi-atom) charge approximation for everything
(solvent, ions, molecules, membrane) for the two states (i) and (ii)
Property (b) similarly uses a hydrophobicity table assigning hydrophobicity
values between 0 and 1 and on a per atom (quasi-atom).
Property (c) uses parallel APBS on the cluster with appropriate dilectric
maps for the two states

We dont need to computer GB energies, or run Smol for binding constants (we know
the approx from the papers ), nor do ion-permeation in the AchR channels.
Furthermore, for now we keep diffusion of Ach on hold...till we complete
the above calculations.

Please let Samrat and I know if you have any further questions.
chandrajit