From owner-chemistry ^at^ ccl.net Thu Apr 12 16:13:01 2012
From: "David Anthony Mannock dmannock[a]ualberta.ca" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Advice on sterol/steroid QC calculations wanted.
Message-Id: <-46685-120412155347-11962-wAHvYlPlU9x2CwGv/gV1hw(_)server.ccl.net>
X-Original-From: "David Anthony Mannock" <dmannock~~ualberta.ca>
Date: Thu, 12 Apr 2012 15:53:42 -0400


Sent to CCL by: "David Anthony Mannock" [dmannock[#]ualberta.ca]
Greetings fellow molecular chemists! We have recently completed a series of experiments on a range of 30+ sterol structures in model lipid bilayers using calorimetric and spectroscopic techniques with considerable help from a student. I have already performed a number of DFT calculations using the opt/freq option in G09 and B3LYP/6.31 or 311++ (d,p). [I hope I got that right!] This has generated a number of conformations for each sterol/steroid structure in the ground state and I am not unhappy with the results. However, I need advice on a number of issues. [I do have the Handbook of computational chemistry (Cook) and Electronic Structure Modeling (Shillady)for back up].

1) Is this approach sufficient to examine the electronic structures of the various sterol/steroid conformations that are evident? Would similar calculations with AIM be beneficial either in providing more accurate/realistic orbital energies or would a Hirschfeld type of analysis be more appropriate?

2) I have seen various messages here on conformations in excited states and energies. What is a good approach in such calculations in G09?

3) Sterols exhibit definite anomeric electronic effects that interact with nearby orbitals originating from double bonds. There are also possible inter- and intra-molecular CH-pi interactions present in some molecules. What is the best calculation solution?

4) Similarly in some of the steroids, resonance effects exist. I am not clear whether these would be covered in calculations of the excited states.

5) With 8-cores some calculations take a week or more. Upgrading to 12 and now 64-cores helps for those subroutines that can run in parallel in G09, but I am wondering if there is a way to break down this extensive computation into parts to decrease the computation time? I am thinking that I could perform some calculations on my 12-core server and others on the 64-core machine. I am thinking that this will be possible by using a line such as "(guess = read)" to access a checkpoint file.

6) I have an Nvidia M2075 card and I know there are mp software solutions which use CUDA that are free for academic use. Any suggestions would be welcome, as I am not familiar with using that software.

Finally, I should add that while I have learned a lot, I know just enough to be dangerous! Guidance from experts would be most helpful in getting this done correctly.

Thanks in advance, Dr David Mannock

dmannock*o*ualberta.ca