Advance 150K. On Tue, Feb 22, 2011 at 09:23:14AM -0600, [email protected] wrote:
Hello,
A change in allocation has been requested:
Requester: roux (Benoit Roux) Project: Drude Title: Development and validation of new polarizable force field for molecular dynamics Description: At the present time, MD simulations are not only limited by the computational resources but also by the physical correctness and accuracy of the underlying atomic models. Without a systematic approach to generate, test and validate the accuracy of the force fields, the value of MD simulations will always remain in question. The development of potential functions for computer simulations has a long history and is still a very active field. Essentially all of the MD simulations of complex molecular systems (biological or not) are currently carried out using fixed-charge non-polarizable force fields, even though there is a broad consensus that electronic polarization effect ought to be included. The important role of polarization is particularly obvious for self-assembling amphiphilic molecules, containing polar or charged groups as well as nonpolar moieties (see below). A number of research groups are working at developing new algorithm to treat polarization, eit her with inducible point dipoles, fluctuating charges, or classical Drude oscillators. The latter approach, which we have adopted, is the most advantageous due to its simplicity and computational efficiency.
The goal is to develop, optimize, and validate the functional form and parameters of a new force field accounting for induced polarization in molecular dynamics simulations. We are particularly interested in ion solvation properties.
# computational methods
The computational method involves ab initio quantum mechanics, as well as classical molecular dynamics simulations and free energy perturbation. The induced polarization is represented by introducing a small auxiliary charged particle attached to the nucleus by a spring. The pair forms a Drude oscillator. It can be shown that this construction accounts properly for the physics of induced polarization in molecular interactions.
# scalability issues
The new force field is developed to be implementable in a wide range of existing molecular dynamics codes. Currently, the model is supported by CHARMM, which has modest scalability. Our initial implementation of the methods in NAMD has allowed to run some benchmark systems with 75,000 water molecules with the polarizable force field. These NAMD simulatinos scale up to 1,000 cores without problems.
# experiments planned
We are also developing ion solvation models in water, liquid N-methylacetamide, and liquid ethanol. Those are needed to model biomolecular systems. The work will comprise
- divalent ions solvation in N-methylacetamide - CPMD run of K+ in ethanol - CPMD run of Na+ in ethanol - high level ab initio on small clusters - free energy perturbation MD of K+ in ethanol - free energy perturbation MD of Na+ in ethanol - osmotic pressure MD for NaCl and KCl - conductivity of KCl and NaCl
# software requirements
We use Gaussian, Qchem, CPMD, CHARMM, and NAMD.
# sizes of calculations run on and/or planned for Fusion or other systems
On single MD runs, we expect to use up to 256 or 512 cores in parallel. The CPMD does not scale as well (perhaps up to 64). The FEP simulations are trivially distributed (thermodynamic integration). The osmotic pressure and the conductivity require several MD at increasingly high ionic concentrations with large systems.
# expected number of project members:
The number of members is expected to be 5-6, including Benoit Roux, Karen Callahan (ions in ethanol), Yun Luo (osmotic pressure), Chris Rowley (divalent ions), from the University of Chicago.
REFERENCES
Yu, H; Mazzanti, CL; Whitfield, TW, et al. A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Volume: 132 Issue: 31 Pages: 10847-10856 Published: 2010
Baker, CM; Lopes, PEM; Zhu, X, et al. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 6 Issue: 4 Pages: 1181-1198 Published: 2010
Yu, HB; Whitfield, TW; Harder, E, et al. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 6 Issue: 3 Pages: 774-786 Published: 2010
Harder, E; MacKerell, AD; Roux, B Many-Body Polarization Effects and the Membrane Dipole Potential. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Volume: 131 Issue: 8 Pages: 2760-+ Published: 2009
Harder, E; Anisimov, VM; Whitfield, TW, et al. Understanding the dielectric properties of liquid amides from a polarizable force field. JOURNAL OF PHYSICAL CHEMISTRY B Volume: 112 Issue: 11 Pages: 3509-3521 Published: 2008
Whitfield, TW; Varma, S; Harder, E, et al. Theoretical study of aqueous solvation of K+ comparing ab initio, polarizable, and fixed-charge models. JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 3 Issue: 6 Pages: 2068-2082 Published: 2007
Current: undetermined amount Justification: We have an excellent track record of publication in this field, and we will make good use of the allocated time. The project involves a variety of different computations (MD, ab initio, CPMD), which are all very important to develop good models. We could easily ask for more resource, and we will definitely utilize all the allocation requested.
Requested: 450000
A specific reason has been given: This allocation is currently negative. Can we reset this to 450,000 to allow us to pursue the work on the drude force field?
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