From owner-chemistry@ccl.net Thu May 18 13:21:00 2006 From: "Ross Walker ross]|[rosswalker.co.uk" To: CCL Subject: CCL: QM/MM computational cost? Message-Id: <-31779-060518130944-6256-Dz/DSR6zbs1p1wuH+j+Abw],[server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 18 May 2006 10:09:33 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross|*|rosswalker.co.uk] Hi Nathan, > Greetings CCLers. Can anyone point me to a reference discussing the > computational cost of QM/MM simulations and how it scales > with size of the > components? I have some experience with quantum chemistry > simulations, as > well as molecular dynamics simulations, but I'm new to QM/MM > and am being > asked as part of a proposal I'm writing to discuss the > computational cost o= > f > the calculations I want to do. Right now the plan is to > solvate a simple 6 > atom quantum mechanical system with approximately 1000 TIP4P water > molecules. This really depends on the type of QM calculation you plan on doing which you don't state. Semi-empirical is significantly cheaper than full ab initio. For what you suggest above if you wanted to do semi-empirical you can use Amber 9 and the computational cost will be about 6% more than doing the calculation classically. You can probably go to about 90 QM atoms or so before it even starts to become expensive. Plus you can do a simulation with a full treatment of electrostatics and periodic boundaries for both the QM and MM regions using PME. Without a PME treatment you will need to use an infinite (i.e. no) cutoff and probably add an implicit solvent treatment for the gas phase region of your system to get meaningful results. Using a cut off with gas phase / water cap simulations introduces serious artefacts into your simulation and can completely invalidate your results. Hence often it can be quicker to do a full PME treatment than to run the gas phase non-periodic simulation. A lot of work has been put into making Amber 9's QM support as fast as possible while preserving accuracy in the gradients. It is around 10 times quicker than Amber 8 and Charmm c32. The Amber 9 QMMM implementation is currently being added to Charmm and will I believe be released shortly. As a quick guide here are the timings I got for two water molecules treated with PM3 and then solvated with a rectangular box consisting of 332 TIP4P water molecules. PME was run with an 8 angstrom MM and QM direct space cut off, shake was used for both the MM and QM region, langevin thermostating was used at 300K and a timestep of 2fs was used. For the gas phase simulation I used an infinite MM and QM cut off. The default SCF convergence of 1.0x10-8 KCal/mol was used. This is for a pentium-D 3.4GHz 2MB L2 cache machine. Time is for 2000 steps = 4ps. 1 cpu 2 cpu's time(s) ns/day time(s) ns/day PME classical = 39.99 8.64 23.35 14.80 PME QMMM = 62.15 5.56 40.15 8.83 Gas phase clas= 123.67 2.79 64.48 5.36 Gas phase QMMM= 130.99 2.64 70.12 4.93 So for the system you want to study it really won't cost you much at all. However, if you want to do a full abinitio treatment then it could get very expensive. All the best Ross /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross[]rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.