Granted 100k to entropy - JB On Mon, Jun 8, 2015 at 1:51 PM, Bair, Raymond A. <[email protected]> wrote:

A small request, so lets approve it.

Ray

On 6/5/15, 9:10 PM, "[email protected]" <[email protected]> wrote:

...

Hello,

A change in allocation has been requested:

Requester: sunhwan (Sunhwan Jo) Project: entropy Title: Quantifying protein-protein binding with greatly scalable multiple copy algorithms of NAMD Description: In PMF-based framework, a set of geometric and conformational restraints is applied to the proteins to reduce sampling noise and accelerate the convergence of the resulting free energy profile. These biases are rigorously accounted for to produce the absolute binding free energy. To enhance the PMF convergence, we will combine the umbrella sampling with Hamiltonian and temperature (ℋ and T) replica-exchange molecular dynamics (REM) algorithm. In the US/(ℋ,T)-REMD simulation approach, multiple copies of the molecular systems are simulated concurrently, but
all with different
conditions, e.g., umbrella potential (Hamiltonians) or temperature. Attempts are periodically made to exchange configurations between different systems using a Metropolis-type Monte Carlo acceptance criterion, insuring Boltzmann-weighted statistics. Such REMD
methodology is extremely scalable, yet also very effective to sample a rugged free energy surface.

We anticipate the simulation systems will be comprised of ~50,000 atoms and using at least 255 replicas concurrently. Because of its large size, we plan to use primarily Mira for production and Fusion will be used for initial system preparation and development of enhanced methodology in PMF-based framework. All planned simulations will be carried out by the open-source NAMD molecular dynamics software. The software engine used for the planned simulations is NAMD 2.10 with Charm++ 6.4.0. We have tested t he performance on BG/Q Mira. The scaling of parallel performance was linear up to 512 cores for our test system comprised of 100,000 atoms without using restraint potential and achieved the speed of about 0.025 s/step. Using restraint potential reduces the parallel performance significantly (~0.2 s/step).

The expected number of project member is 3. I, Sunhwan Jo, recently joined LCF as a postdoctoral appointee and will be the main person performing code improvement and algorithm development under the supervision of Wei Jiang (LCF) and Benoit Roux (UChicago).

Current: undetermined amount Justification:

Requested: 100000

A specific reason has been given: A paper is published from this calculation (http://pubs.acs.org/doi/abs/10.1021/ct501034w) and we are extending the project to perform more sophisticated calculation. We have completed ~50% of the calculation needed but need more time to finish the calculations.

This needs to be approved and the final allocation amount decided upon.

Thank You, The LCRC Accounts System

_______________________________________________ allocations-admins mailing list [email protected] https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins