March 2011 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Request: LiAirLDRD-TMOxides
by accounts＠lcrc.anl.gov 21 Mar '11

21 Mar '11

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Maria Chan Applicant's institution: ANL Applicant's division: CNM Project Name: LiAirLDRD-TMOxides Project title: Investigations of transition-metal oxides as electrocatalysts for Li-air batteries Associated funding: Argonne LDRD Other Systems: CNM Carbon Science: Argonne has recently funded a Grand Challenge LDRD project in the development of Li-air batteries [1]. Li-air batteries offer significantly higher capacities than their Li-ion counterparts, but there are significant technological challenges before widespread applications are feasible. Among the challenges are large polarizations between charge and discharge and limited cycleability. Recently, our experimental collaborators at Argonne, Lynn Trahey and Mike Thackeray, have found [2] that the use of Li-Fe/Mn-oxides as electrocatalysts useful both in reducing polarization and improving cycleability, when compared with carbon. The mechanism of this significant improvement remains unknown, and first principles computation is important in unraveling this mystery. The electrocatalysts considered are Fe and Mn oxides that incorporate or can accomodate Li2O in their structures. The goal of our project is to investigate the thermodynamics and mechanism of removal and insertion of Li and Li-O_x species from and into these transition metal (TM) oxides, in order to understand their underlying role of in the Li-O2 reaction and suggest improvements. The calculation of total energies of these TM oxides at various stages of Li/Li-O_x removal and insertion will allow us to associate the thermodynamic phases with a equilibrium voltage, which will be compared with the voltages of Li2O and Li2O2 formation. Additional information from atomic radial distribution functions and XANES spectra will corroborate the calculated configurations and electronic structures with experimental characterization carried out at the APS. Calculations involving Li-O_x species on the surfaces of these TM-oxides will allow the deduction of thermodynamic barriers and overp otentials for Li-O2 reactions. Finally the kinetics of Li and Li-O_x transport in these structures are investigated to delineate where transport may be limited. [1] http://www.anl.gov/Media_Center/News/2009/batteries090915.html [2] L. Trahey, C. S. Johnson, J. T. Vaughey, S.-H. Kang, L. J. Hardwick, S. A. Freunberger, P. G. Bruce,b, and M. M. Thackeray, "Activated Lithium-Metal-Oxides as Catalytic Electrodes for Li–O2 Cells" Electrochemical and Solid-State Letters, 14 (5) A64-A66 (2011). Project description: We will use density functional theory (DFT) with the Hubbard U (+U) correction and hybrid functionals which have been demonstrated to produce accurate energetics and reasonably accurate electronic structures in correlated systems such as TM oxides. We will perform DFT+U total-energy calculations involving Li-O_x insertion and removal from Fe/Mn oxides, which involves significant configurational sampling. An estimated 500 such calculations requiring 100-500 core-hours each are needed. Where feasible, accurate energetics and electronic structures will be obtained from optimal structures using hybrid functionals, which are more computationally expensive than DFT/+U. Approximately 50 such calculations requiring 1000-3000 core-hours each are needed. Ab initio molecular dynamics calculations will be used to extract the radial distribution functions and diffusion coefficients. Approximately 100 such calculations requiring 500-1000 core-hours each are needed . Using the projector-augmented wave method, only valence electrons will be included which reduces computational costs. We will use well-established DFT codes VASP and GPAW, which use a plane wave basis set and real space grids respectively. For large systems such as nanostructures, VASP has been tested on Fusion for computation involving systems with up to 7000 electrons. For routine calculations, hard scaling efficiency of 70%-80% has been demonstrated for 64 to 128 cores compared to 8 cores, thus enabling efficient calculations of large numbers of configurations. Project URL: Requested allocation: 325000 Justification: The requester has used 1366 hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 21 Mar '11

21 Mar '11

Hello, A change in allocation has been requested: Requester: mchan (Maria Chan) Project: CEES-Si Title: Investigations of silicon surfaces and interfaces for lithium ion batteries Description: We will use total energy DFT calculations to evaluate the adsorption and absorption energy and nudged elastic band migration barriers of Li on and near Si (100), (111) and (110) surfaces with low energy reconstructions. We will also calculate the effects of adsorbed and substitutional impurities on the energetics and kinetics. I will consider 6 types of impurities, 2-3 types of reconstruction per surface orientation, and 10-20 Li position, and combinations thereof. This will amount to 1000-2000 calculations of 100-200 core-hours each. Vibrational frequencies from DFT forces dynamical matrices will be computed in order to aid comparisons with experiments. In addition, energetics and kinetics of Li in nanowires, at the interface between crystalline and amorphous silicon, and between Si and inorganic minerals found to be present at electrode interfaces, will be studied. Interface and nanowire calculations will each consume 500-2000 core-hours and 50-100 calcu lations will be performed. Using the projector-augmented wave method, only valence electrons will be included which reduces computational costs. We will use well-established DFT codes VASP and GPAW, which use a plane wave basis set and real space grids respectively. For large systems such as nanostructures, VASP has been tested on Fusion for computation involving systems with up to 7000 electrons. For routine surface calculations, hard scaling efficiency of 70%-80% has been demonstrated for 64 to 128 cores compared to 8 cores, thus enabling efficient calculations of large numbers of configurations. Please note that I am requesting an allocation for FY2011 significantly higher than that will have been used by the end of FY2010 because my FY2010 allocation did not start until March 2010 and from March to September 2010 I still have access to other machines from previous affiliations that I will no longer have access to in FY2011. Current: undetermined amount Justification: Requested: 300000 A specific reason has been given: The scope of the project has been extended to include: (1) the effects of dopants on lithium insertion into Si and (2) automatic lithiation simulations of bulk, surfaces, amorphous-crystalline interfaces, and nanowires. The automatic lithiation algorithm allows the study of thermodynamic stable phases in the process of lithium insertion into Si, and requires a large number of configurational sampling calculations for each initial Si structure. Please note that the initial allocation of 100,000 SUs for this project was exhausted in December 2011, and early release of another 100,000 SUs was requested which was also exhausted. This work is critical to the Center for Electrical Energy Storage (CEES), a DOE Energy Frontier Research Center, since Si is the forerunning alternative to carbon as anode material for Li-ion batteries and CEES is exerting significant experimental efforts in its investigation. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 20 Mar '11

20 Mar '11

Hello, A change in allocation has been requested: Requester: ssom (Sibendu Som) Project: foam-EngineProcesses Title: Assessment of OpenFOAM for different Engine-Process Applications Description: The project is divided into two main parts: In the first part, fundamental studies will be performed to establish flame stabilization and lift-off characteristics of diesel and biodiesel. A new surrogate mixture (methyl decanoate + methyl decenoate + n-heptane) fuel will be used for modeling the combustion characteristics of biodiesel. The major motivation is to develop more predictive and robust sub-models for capturing diesel engine processes. Fairly large chemical-kinetic models, LES turbulence models, fine grid resolution facilitates use of more than one node (8 cores) for simulating these processes. In the second part, the engine full-cycle will be simulated and the effects of the computational grid on the predicted in-cylinder flow at the intake valve closing (IVC) will be analyzed. Furthermore, the mixture formation process of a gaseous fuel direct-injection will be studied. Here again, the use of computational grids characterized by very high resolution (as expected for the analysis of supersonic jets, jet-to-jet interaction and wall-jet impingement) will require parallel computing (1-2 nodes, 8-16 cores). Current: undetermined amount Justification: Requested: 90000 A specific reason has been given: Our usage was low in 2011 since we were not able to dedicate enough resources. From April we would be performing scalability studies with OpenFOAM and expect to use lot of core-hours. Also we are hiring a summer intern to work exclusive on OpenFOAM from May. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 18 Mar '11

18 Mar '11

Hello, A change in allocation has been requested: Requester: tslee (Tsung-Shung Lee) Project: EBAC Title: Analysis of Nucleon Resonances Description: The objectives of Analysis of Nucleon Resonances (N*) are twofold. The first is to perform dynamical coupled-channels analysis of meson production reaction data for extracting the parameters of nucleon resonances. The second objective is to develop theoretical interpretations of the determined resonance parameters in terms of hadron structure calculations such as the constituent quark model and Lattice QCD calculations. This project will provide information for understanding the non-perturbative aspects of QCD. In particular, the extracted N-N* form factors will reveal the dynamical origins of quark confinement and the meson cloud associated with the spontaneously breaking of chiral symmetry. This project is needed to reach milestones HP3 and HP7 by 2012 set in DOE's long-range plan of 2010. Current: undetermined amount Justification: The analysis will be carried out by solving a large set of coupled integral equation in momentum-space an performing chi-squared fits , with about 200 parameters, to very extensive world data of pion-nucleon scattering and electromagnetic meson production reactions. The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated many times in searching the best-fit parameters in chi-squared fit to very extensive data (about 60,000 data points) using MINUIT Requested: 100000 A specific reason has been given: The EBAC project has been extended to analyze the data of meson resonances in three-pion production reactions. This additional work is crucial for making predictions for new experiments with 12 GeV upgrade at Jefferson Laboratory, and analyzing rather extensive data from B meson factories to study CP violation. The calculations require solving time-cosuming three-particle scattering equations, and we thus need additioanl allocation in the second half of 2011. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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Re: [allocations-admins] Fwd: [lcrc-support #67479] request for additional allocation
by Bair, Raymond A. 18 Mar '11

18 Mar '11

OK with me. On 3/18/11 4:38 PM, "John Valdes" <valdes(a)mcs.anl.gov> wrote: > Bin Liu is asking for 20K to be advanced to his project dft_biomass. > The project is currently negative -273 corehours. He knows that new > allocations will be given at the end of March, so this is hold him > over until then. He requested 600K for the year, was granted 240K for > the 1st half, and was advanced 80K at the end of Dec. > http://www.lcrc.anl.gov/jazz/CSAC/project-reports-2011/Individual/dft_bioma…. > php > > OK to advance 20K? > > John > > ----- Forwarded message from Bin Liu <bliu(a)anl.gov> ----- > > Date: Fri, 18 Mar 2011 14:01:35 -0500 > From: Bin Liu <bliu(a)anl.gov> > To: support(a)lcrc.anl.gov > Subject: [lcrc-support #67479] request for additional allocation > Reply-To: support(a)lcrc.anl.gov, Bin Liu <bliu(a)anl.gov> > > Hi, > > Due to a recent heavy use of my DFT_biomass account on fusion, the > balance has reached a minimum. I wonder if I can request some additional > hours (say, 20,000) to make sure that the calculations can keep running > this weekend. Thanks very much! > > Best, > Bin > > > -- > ~~~~~~~~~~~~~~~~~~~~~~~ > Bin Liu > Postdoc appointee > Argonne National Laboratory > 9700 S. Cass Ave. Bldg 440 > Argonne, IL 60439 > Work: 630-252-5378 > email: bliu(a)anl.gov > ~~~~~~~~~~~~~~~~~~~~~~~ > > > > ----- End forwarded message ----- > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4126 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751

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Fwd: [lcrc-support #67479] request for additional allocation
by John Valdes 18 Mar '11

18 Mar '11

Bin Liu is asking for 20K to be advanced to his project dft_biomass. The project is currently negative -273 corehours. He knows that new allocations will be given at the end of March, so this is hold him over until then. He requested 600K for the year, was granted 240K for the 1st half, and was advanced 80K at the end of Dec. http://www.lcrc.anl.gov/jazz/CSAC/project-reports-2011/Individual/dft_bioma… OK to advance 20K? John ----- Forwarded message from Bin Liu <bliu(a)anl.gov> ----- Date: Fri, 18 Mar 2011 14:01:35 -0500 From: Bin Liu <bliu(a)anl.gov> To: support(a)lcrc.anl.gov Subject: [lcrc-support #67479] request for additional allocation Reply-To: support(a)lcrc.anl.gov, Bin Liu <bliu(a)anl.gov> Hi, Due to a recent heavy use of my DFT_biomass account on fusion, the balance has reached a minimum. I wonder if I can request some additional hours (say, 20,000) to make sure that the calculations can keep running this weekend. Thanks very much! Best, Bin -- ~~~~~~~~~~~~~~~~~~~~~~~ Bin Liu Postdoc appointee Argonne National Laboratory 9700 S. Cass Ave. Bldg 440 Argonne, IL 60439 Work: 630-252-5378 email: bliu(a)anl.gov ~~~~~~~~~~~~~~~~~~~~~~~ ----- End forwarded message -----

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 17 Mar '11

17 Mar '11

Hello, A change in allocation has been requested: Requester: jellinek (Julius Jellinek) Project: Comp_Nanocatalysis Title: Theoretical/Computational Studies of the Fundamentals of One-Component and Alloy Metal Based Nanocatalysis Relevant to Alternative Sources of Energy Description: The subject of this project is structural, electronic, and chemical reactivity properties of one-component and alloy metal nanocatalysts, both gas phase and deposited on oxide supports. The complexity of these systems stems from the fact that even for a one-component catalytic cluster or nanoparticle the number of different possible structural forms (isomers) is very large. For the case of alloys particles, the complexity increases even further as each isomeric form gives rise to a large number of secondary structures (homotops) that differ by the placement of the different types of atoms between the sites of that isomer. As a consequence, the configuration space that has to be searched is immense. We are using the parallelized version of the NWChem package installed on Fusion. The current work focuses on pure Pt and Mo and mixed Pt/Mo clusters. So far we have covered the size range from 2 to 13 atoms and made some test runs on a 55 atom cluster. The cases of l ow or no symmetry are particularly problematic. Even for a system as small as a 13-atom Pt cluster we repeatedly encountered references to “segmentation error”. The largest number of processors we have used so far is 128. The reason for this is not lack of scalability in performance, but simply the desire to save the very limited resources we have been allocated so far. Our performance tests indicate that we could use profitably hundreds or even thousands of processors in runs on systems with about 50-100 atoms. Our plans are to extend our studies to this size range and beyond. In addition, we plan to add in the computations also the atomistic representation of the supports. The expected number of project members is 4. Current: undetermined amount Justification: The allocation request is based on estimates made on Fusion and on Carver at NERSC. Tests on Pt_12Mo cluster with the Stuttgart pseudopotential and a basis set of 38 contracted functions per atom performed with 32, 64, and 128 processors indicate full parallel scaling efficiency. Tests on a 55 atom cluster with 128 and 200 processors give a comparable scaling. Requested: 621000 A specific reason has been given: We were "holding back the horses" in the first half of FY11, yet we ran out of time (allocation) by Feb. 18, 2011. The work planned for the second half of FY11 is substantially more demanding computationally, because we will focus on pure and mixed nanocatalysts of larger sizes (50 atoms and more) and we will expand the studies to include their chemical reactivity with various molecules. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 16 Mar '11

16 Mar '11

Hello, A change in allocation has been requested: Requester: roux (Benoit Roux) Project: kv Title: Studies of voltage-vgated potassium channel Description: Voltage-gated potassium (Kv) channels are membrane proteins that respond to changes in the transmembrane potential by altering their conformation to allow the passive conduction of K+ ions across the cell membrane. These channels are tetrameric proteins, in which each subunit comprises six transmembrane (TM) helical segments (S1-S6). The ion conduction pore is located at the center of the tetrameric structure and is formed by the S5 and S6 helices from the four subunits. The first four segments (S1-S4) in each subunit form a voltage-sensing domain (VSD) that is located in the lipid membrane at the periphery of the central pore domain (PD). Upon depolarization of the membrane, the VSD in each subunit undergoes a voltage-dependent transition from a resting to an active conformation, which then leads the opening of the intracellular gate of the ion conduction pore. The conformational changes associated with the activation of Kv channels result in the transfer of an electric charge Delta-Q across the membrane, that can be measured experimentally as a small transient capacitive current. In the Shaker K+ channel, the "gating charge" corresponds to the transfer of 12-14 elementary charge (e) along the transmembrane electric field. Correspondingly, a change V in the membrane potential shifts the relative free energy of the closed and open conformations by V*Delta-Q. The gating charge DeltaQ is, thus, a key concept to explain how channel activation is coupled to the membrane potential. Initially postulated by Hodgkin and Huxley in 1952, it was first detected and measured more than 20 years later by Armstrong and Bezanilla. Ultimately, explaining the voltage-gating mechanism of Kv channels in molecular terms requires gaining knowledge of the active and resting conformations, and then showing how those conformations are able to account for the experimentally observed gating charge Delta-Q. Our strategy is to first carefully construct atomic models of the active and resting states of Kv channels that are consistent with all available experimental information using protein structure prediction algorithms. We also have a novel method to compute the gating charge using all-atom MD. Pathak et al. have generated detailed atomic models of Kv1.2 in the open/active and closed/resting states using the Rosetta-Membrane structure prediction program. The model of the open/active state complements the information missing from the X-ray structure of the Kv1.2 channel used as a template, while the S1-S2, S2-S3, and S3-S4 loops in the voltage sensing domain were modeled de novo. These results offer a promising starting point to expand our understanding of voltage gating in Kv channels. Some critical issues must be addressed. Recently, the stability of those structural models in the complex dynamical environment of the lipid bilayer was ascertained using molecular dynamics (Khalili-Araghi et al, 2010) and the gating charge was calculated using a new theory of the membrane potential (Roux, 2008). Our long-term goal is to refine the atomic models of the closed/resting and open/activated states and test their ability to account for the experimentally observed gating charge using all-atom MD and explicit lipid membrane environment. In the coming year, we have 3 specific sub-projects: 1) We want to incorporate additional experimental constraints in the refinement of the resting down-state of the voltage sensor (Macpos et al, 2007). Ernesto Vargas (a graduate student at the University of Chicago) is carrying out this project. 2) We want to predict the effect of side-directed mutations on the channels, namely the effect of substitution along the transmembrane helix S4. David Medovoy (a graduate student at the University of Chicago) is carrying out this project. 3) We want we want to refine the 3d structure of the bacterial voltage-gated channel KvAP using electron paramagnetic resonance (EPR). We will use a new mmethod that has been develop by us (Sompornpisut et al, 2008) and tested on other channels (Vasquez et al, 2008). This work will be carried out by a visiting scholar (Rong Shen). We had originally requested 250K nodehours for the fiscal year, but only half of that, 125K was granted by the Allocation committee. These systems run NAMD on 25 cores at a rate of about 1 day/nanosecond of MD. For a total of 50 ns of simulation total for the 3 projects means that we need about 300,000 nodehours. REFERENCES Pathak, M.M., V. Yarov-Yarovoy, G. Agarwal, B. Roux, P. Barth, S. Kohout, F. Tombola, and E. Y. Isacoff. (2007). "Closing in on the Resting State of the Shaker K+ Channel." Neuron 56, 124-140. Campos, F.V., B. Chanda, B. Roux, and F. Bezanilla. (2007). "Two Atomic Constraints Unambiguously Position the S4 Segment Relative to S1 and S2 Segments in the Closed State of Shaker K Channel." Proceedings of the National Academy of Sciences of the United States of America 104, 7904-7909. Sompornpisut, P., B. Roux, and E. Perozo. 2008. Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data. Biophys 95:5349-5361. Vasquez, V., M. Sotomayor, D. M. Cortes, B. Roux, K. Schulten, and E. Perozo. 2008. Three-dimensional architecture of membrane-embedded MscS in the closed conformation. J Mol Biol 378:55-70. Pan, A.C., D. Sezer, and B. Roux. (2008). "Finding Transition Pathways Using the String Method with Swarms of Trajectories." J Phys Chem B 112, 3432-3440. Roux, B. 2008. The membrane potential and its representation by a constant electric field in computer simulations. Biophys J 95:4205-4216. Khalili-Araghi, F., V. Jogini, V. Yarov-Yarovoy, E. Tajkhorshid, B. Roux, and K. Schulten. 2010. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys J 98:2189-2198. Current: undetermined amount Justification: We had originally requested 250K nodehours for the fiscal year, but only half of that, 125K was granted by the Allocation committee. These systems run NAMD on 25 cores at a rate of about 1 day/nanosecond of MD. For a total of 50 ns of simulation total for the 3 projects means that we need about 300,000 nodehours. For the resources, we expect to be using NAMD runs of up to 256 CPU. This amounts to: 256 CPU * 24 hours * 50 days = ~300,000 Fusion will be an excellent platform to establish and execute the string method algorithm. Requested: 200000 A specific reason has been given: We are reducing our request regarding this project because we can run it on Beagle and on the teragrid and with our INCITE allocation. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 16 Mar '11

16 Mar '11

Hello, A change in allocation has been requested: Requester: roux (Benoit Roux) Project: kcsa Title: Computational study of ion selectivity in the KcsA channel Description: Understanding quantitatively the microscopic factors controlling ion selectivity remains a great challenge. In simple terms, the concept of selectivity means that the "correct" ion, is able to binding more favorably than an "incorrect" ion. At a physical level, it is to be anticipated that energetics and solvation play a key role in this process, although different aspects of energetics may be highlighted by the various experimental methods used to probe the system. Some experimental measurements are more sensitive to the relative depth of free energy wells, while others are more sensitive to the relative height of free energy barriers. In the case of ion channels, the large hydration energy of the ions contrasts with the small free energy barriers necessary for the fast conduction observed experimentally. This implies that ion-protein association is ultimately controlled by a delicate balance of very strong interactions. Frequently, permeation involves th e partial dehydration of an ion, followed by the binding to a proteinaceous environment. This archetype is well illustrated by the crystal structure of the KcsA channel. The pore of the KcsA channel comprises a wide aqueous vestibular entryway, lined by non-polar residues on the intracellular side, leading up on the extracellular side to a narrow region lined by backbone carbonyl oxygens. This region of the pore, formed by the residues corresponding to the signature sequence TTVGYG common to all K+ channels, acts as a "selectivity filter" by allowing only the passage of nearly dehydrated K+ ions across the cell membrane. In such narrow molecular pores, a permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with the backbone carbonyl oxygens. The most informative strategy to address such issues is to compute the multi-ion PMF corresponding to the microscopic process in question (Berneche and Roux, Nature 2001). In particular, the calculation of the PMF enables us to pin-point the location of the largest barrier opposing the passage of a single Na+ ion while there are two K+ ions elsewhere in the pore. We carry those type of calculations using umbrella sampling MD simulations. Another strategy is free energy perturbation (FEP), which allows to compute the relative free energy of different ions at precise location in the pore. There are 2 sub-projects: 1) Compute the multi-ion PM for Na+ permeation through the KcsA channel using the open state structure that was recently determined by X-ray crystallography in the Perozo laboratory. We have already done a similar calculation for the KcsA in the closed state (Egwolf and Roux, JMB 2010). Umbrella sampling MD simulations are used to obtain W(z1,z2,z3) the 3-ion PMF function of the coordinate of the 3 ions in the selectivity filter. To understand the effect of selectivity, two systems must be considered: with 3 K+ ions, and with 1 Na+ and 2 K+ ions. Based on our experience with similar computations, we know that a grand total of 3931 MD window simulations is needed for two systems. Each window should be simulated for 0.6 ns, the first 0.1 ns being used for equilibration and the last 0.5 ns for sampling proper, for total aggregate MD simulation time of 2.4 microseconds for each of the two systems. The unbiased 3D PMFs are then calculated using the weighted histogram method ( WHAM). The simulations are generated with NAMD, which is the most efficient program for classical MD. 2) Use FEP to compute the relative free energy of Na+ and K+ in a KcsA pore with DFT/MM simulations. For this computation we are using CHARMM combined with the DFT program DEMON (developed by Denys Salahub in Calgary). This enables us to treat the ions and the nearby protein atoms with DFT and the remainder with the force field of molecular dynamics. Software requirements NAMD, CHARMM, DEMON Expected number of project members: Benoit Roux, David Medovoy (multi-ion PMF calculation) and Chris Rowley (selectivity with density function theory and MD force field) REFERENCES Noskov, SY; Berneche, S; Roux, B Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. NATURE Volume: 431 Issue: 7010 Pages: 830-834 Published: OCT 14 2004 Egwolf, B; Roux, B Ion Selectivity of the KcsA Channel: A Perspective from Multi-Ion Free Energy Landscapes. JOURNAL OF MOLECULAR BIOLOGY Volume: 401 Issue: 5 Pages: 831-842 Published: 2010 Current: undetermined amount Justification: The umbrella sampling calculations described here constitute a major part of the PhD thesis of David Medovoy, a graduate student in Biophysics at the University of Chicago. The total requested allocation for this project is: 500,000 SU = (3931 windows) * (0.6 ns/window) * ((8*cores)*(12 hour)/ns). The planned FEP simulations for with DFT/MM will be carried out by Chris Rowley, a postdoc in the lab who has a fellowship from the Canadian NSERC. His work will be a new attack on the problem. Never before has someone computed relative free energies in those channels with DFT/MM. We anticipate this those FEP calculations will require about 500,000 SUs during the year. Demon scales up to about 64 processors, but we are investigating the dependencies on grid density (in DFT) to see how it affects the performance. Requested: 100000 A specific reason has been given: This is the other big project that we wish to carry out on fusion because it is our best platform. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 16 Mar '11

16 Mar '11

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: 1000000 A specific reason has been given: Fusion appears as a prime platform to pursue our work on the polarizable force field (which is supported by my LDRD). The allocation is needed for a big push before the end of the summer. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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