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

[LCRC Accounts] Yearly Allocation Request from kv
by accounts＠lcrc.anl.gov 20 Sep '11

20 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Benoit Roux Project Name: kv Division: BIO Project title: Studies of voltage-gated potassium channel Associated funding: NIH/NIGMS, R01-GM062342 "Computational studies of ion channels" INCITE from Office of Science Other Systems: BG/P, NCSA, PSC, KBT Science: Molecular dynamics of membrane proteins that are affected by the transmembrane voltage Project description: We are closing this project for now. Project URL: http://thallium.bsd.uchicago.edu/RouxLab/ Current FY Hours Used: undetermined amount New FY Requested allocation: 0 Q1: 0 Q2: 0 Q3: 0 Q4: 0 Justification: Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from nachbac
by accounts＠lcrc.anl.gov 20 Sep '11

20 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Benoit Roux Project Name: nachbac Division: BIO Project title: selectivity of the sodium channel Associated funding: NIH R01-GM062342 Other Systems: Science: Understanding quantitatively the microscopic factors giving rise to Na+ selective channels is mysterious. For a long while, we had only K+ selective channels (such as KcsA). Just recently, the X-ray structure of a Na+ selective channel was determined. It is related to the NachBAC channel (Na+ Channel from bacteria). Project description: The most informative strategy to address the issue of Na+ selectivity in NachBAC 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 K+ ion relative to Na+ in the channel, thus explaining while the channel becomes selective from the free energy profile. We can carry those type of calculations using our new and highly scalable method called umbrella sampling with replica-exchange MD simulations that is implemented in CHARMM/REPD. We will compute the potential of mean force to ascertain the mechanism of ionic selectivity through the narrow pore. We need to compare permeation of Na+ (the good ion) against K+ (the bad ion). Thus, we need a 1-ion PMF for Na+ and for K+ going through the pore. And we need 2-ion PMF going through the pore because we do not know yet if the permeation mechanism is a one- or two-ion mechanism. For the 1-ion potential of mean force of Na+ through the channel: 60 windows/replica One replica use one node (8 cores). Sampling of 3 ns takes 150 hours. Total needed: 150*60*8 = 72,000 core-hours For the 1-ion potential of mean force of K+ through the channel: 60 windows/replica One replica use one node (8 cores). Sampling of 3 ns takes 150 hours. Total needed: 150*60*8 = 72,000 core-hours For the 2-ion potential of mean force with Na+ through the channel: 350 windows/replica One replica use one node (8 cores). Sampling of 1 ns takes 50 hours. Total needed: 50*350*8 = 140,000 core-hours For the 2-ion potential of mean force with K+ through the channel: 350 windows/replica One replica use one node (8 cores). Sampling of 1 ns takes 50 hours. Total needed: 50*350*8 = 140,000 core-hours analysis in 3 Qtr 3 * 25,000 GRAND TOTAL NEEDED: 500,000 core-hours. Project URL: http://thallium.bsd.uchicago.edu/RouxLab/ Current FY Hours Used: undetermined amount New FY Requested allocation: 500000 Q1: 425000 Q2: 25000 Q3: 25000 Q4: 25000 Justification: This is a very very competitive project, as others are racing to produce calculations. This is why our request is biggest at the early stage of the project. We are ready to proceed with these calculations as soon as we have the allocation. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from Drude
by accounts＠lcrc.anl.gov 20 Sep '11

20 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Benoit Roux Project Name: Drude Division: BIO Project title: Development and validation of new polarizable force field for molecular dynamics Associated funding: LDRD: 2009-047-R1, "Novel Computing Methodologies for the Simulation of Complex Molecular Systems" NIH grant from NIGMS R01-GM072558: Polarizable Force Field For Proteins and Lipids Other Systems: BG/P, NCSA, PSC, KBT Science: The functional form and parameters of a new force field accounting for induced polarization in molecular dynamics simulations must be developed, optimized, and validated for various biomolecular systems. Project 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 polarizati on, either 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, and in NAMD. Scalability is typically better with NAMD. But that is for simple brute force simulations. For alchemical free energy perturbation, we can run replica-exchange simulations FEP/REMD using CHARMM/REPD, which is extremely scalable. # computations planned We are now refining ion solvation models in liquid N-methylacetamide (NMA). We also need to study methyl-acetate, which is an imprtant fragment of phospholipid molecules forming membrane bilayers. Those are needed to model biomolecular systems. The work will comprise - high level ab initio on small clusters - FEP for monovalent ions solvation in NMA - FEP divalent ions solvation in NMA - FEP of methylacetate in water # software requirements We use Gaussian, Qchem, CPMD, CHARMM, and NAMD. # sizes of calculations run on and/or planned for Fusion or other systems The work always starts with some ab initio in small clusters. The most demanding part of the project corresponds to the large number of FEP computations needed to fully optimize the force fields. The FEP simulations are extremely scalable via CHARMM/REPD when we carry them as replica-exchange MD. The osmotic pressure require several MD at increasingly high concentrations with large systems. Lastly, we also use CPMD for some systems when required (like we simulated Na+ and K+ in NMA to clarify issues of coordination numbers). # 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. In the coming year we need to parametrize divalent cations solvated in N-methylacetamide. This will require both ab initio calculations as well as solvation free energy computations. Request: The dominant part of the project is the FEP calculations. To estimate the number of SUs, it is sufficient to focus on what is needed for this. For one case, we typically require about 100 trials to scan the space of parameters and search for the optimal model. We have to do five cases (Na+ and K+ in NMA, Ca+2 and Ba+2 in NMA, and methyl-acetate in water). A single solvation FEP/REMD calculation: 75 windows/replica One replica use one node (8 cores). Sampling of 0.1 ns takes 2 hours. Total needed: 75*2*8 = 1,200 core-hours Total needed for one complete parametrization : 120,000 core-hours Total needed for five complete parametrization: 600,000 core-hours. This project is long-term, and the allocation could be evenly divided over each quarter with no problem. RECENT 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 Project URL: http://thallium.bsd.uchicago.edu/RouxLab/ Current FY Hours Used: undetermined amount New FY Requested allocation: 600000 Q1: 150000 Q2: 150000 Q3: 150000 Q4: 150000 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, FEP), which are all very important to develop good models. We will definitely utilize all the allocation requested. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from kcsa
by accounts＠lcrc.anl.gov 20 Sep '11

20 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Benoit Roux Project Name: kcsa Division: BIO Project title: Computational study of ion selectivity in the KcsA channel Associated funding: NIH-GM062342 Other Systems: NCSA, KBT Science: The selective transport of small ions (e.g., Na+, K+) through the KcsA ion channel is characterized quantitatively using computational methods. Project 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. Barium (Ba2+) is a divalent ion that is known to block the normal conduction of K+ ion. Altering the concentration of K+ on one side of the channel release the block by pushing the Ba2+ to the other side. Pushing the Ba2+ can also be done by Na+, but it is more difficult because the channel prefer (is selective) to K+. This technique has been used experimentally to probe the selectivity of the channel for K+ over Na+. But this process is not fully understood at the microscopic level, which undermines a robust interpretation of the experimental results. Our goal is to compute the mechanism of barium blockade in the KcsA channel. The most informative strategy to address issues of ion selectivity is to compute the multi-ion PMF corresponding to the microscopic process in question (Berneche and Roux, Nature 2001). We carry those type of calculations using umbrella sampling MD simulations. Recently, we have been able to do this with the extremely scalable strategy based on hamiltonian replica-exchange MD using CHARMM/REPD. Tasks to do: We will compute the multi-ion PM for a channel blocked by one Ba2+ in the presence of K+. We will also compute the multi-ion PM for a channel blocked by one Ba2+ in the presence of Na+. The comparison between the two PMFs will reveal the microscopic basis for the unblocking effect of the added ion (K+ or Na+). A 2-ion potential of mean force with one Ba2+ and one K+ going through the channel: 350 windows/replica One replica use one node (8 cores). Sampling of 1 ns takes 50 hours. Total needed: 50*350*8 = 140,000 core-hours A 2-ion potential of mean force with one Ba2+ and one Na+ going through the channel: 350 windows/replica One replica use one node (8 cores). Sampling of 1 ns takes 50 hours. Total needed: 50*350*8 = 140,000 core-hours Total needed for this project 280,000 core-hours This project is ready to go, so we could use the resource immediately, starting with the first quarter. Software requirements CHARMM/REPD Expected number of project members: Benoit Roux, and Chris Rowley 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 Project URL: http://thallium.bsd.uchicago.edu/RouxLab/research.html Current FY Hours Used: undetermined amount New FY Requested allocation: 280000 Q1: 200000 Q2: 30000 Q3: 25000 Q4: 25000 Justification: Thank You, The LCRC Accounts System

1 0

Re: [allocations-admins] Fwd: [lcrc-support #87491] Change on allocation time requested
by Bair, Raymond A. 19 Sep '11

19 Sep '11

Yes they can change their request. Ray ----- Original Message ----- From: John Valdes [mailto:[email protected]] Sent: Monday, September 19, 2011 05:51 PM To: allocations-admins(a)lcrc.anl.gov <allocations-admins(a)lcrc.anl.gov> Subject: [allocations-admins] Fwd: [lcrc-support #87491] Change on allocation time requested Here are two changes (reductions) in requested allocations, one for a new project and the other for a renewal. Apparently they didn't want to be a part of the 1M club (ie, give a presentation, as they said they are tied up with other work at the moment). Any objections to reducing these requests to the amounts given below? Comp_Nanocatalysis is a renewal which originally asked for 1.2M Comp_Soft_Catalysts is a new project which originally asked for 1M. John ----- Forwarded message from "Lopez-Encarnacion, Juan Manuel" <JMLopez(a)anl.gov> ----- Date: Mon, 19 Sep 2011 16:15:41 -0500 From: "Lopez-Encarnacion, Juan Manuel" <JMLopez(a)anl.gov> To: support(a)lcrc.anl.gov Cc: jellinek(a)anl.gov Subject: [lcrc-support #87491] Change on allocation time requested Reply-To: support(a)lcrc.anl.gov, "Lopez-Encarnacion, Juan Manuel" <JMLopez(a)anl.gov> Dear Team, Please, can you change our allocation time requested to the new numbers on right in the proposals: 1. Comp_Nanocatalysis (PI: Julius Jellinek) - 998,000 2. Comp_Soft_Catalysts (PI: Juan M. Lopez-Encarnacion) - 980,000 We understand that with these request not presentation is needed. Please, send us an E-mail confirming this change. Thank you, Juan and Julius ----- End forwarded message ----- _______________________________________________ allocations-admins mailing list allocations-admins(a)lists.lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0

[LCRC Accounts] Yearly Allocation Request from lcrc-app-engr
by accounts＠lcrc.anl.gov 19 Sep '11

19 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: John Valdes Project Name: lcrc-app-engr Division: LCRC Project title: LCRC Application Engineer support work Associated funding: Other Systems: Science: Project description: This project will be used by the LCRC application engineers to do support work for users of the LCRC cluster. This support might be in the form of installation and debugging of both LCRC core and user applications, benchmarking and performance analysis, user startup help, etc. Project URL: http://www.lcrc.anl.gov Current FY Hours Used: undetermined amount New FY Requested allocation: 16000 Q1: 4000 Q2: 4000 Q3: 4000 Q4: 4000 Justification: Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from support
by accounts＠lcrc.anl.gov 19 Sep '11

19 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: John Valdes Project Name: support Division: LCRC Project title: Systems administration tasks on the LCRC Cluster(s). Associated funding: Other Systems: Science: Project description: This project will be used by the support team for systems tasks. This will include debugging problems, testing upgrades and modifications, and running scaling and performance tests for diverse areas such as scheduling algorithms, networks, filesystem upgrades, application installations, system management, etc. Project URL: http://www.lcrc.anl.gov Current FY Hours Used: undetermined amount New FY Requested allocation: 8000 Q1: 2000 Q2: 2000 Q3: 2000 Q4: 2000 Justification: Thank You, The LCRC Accounts System

1 0

Fwd: [lcrc-support #87491] Change on allocation time requested
by John Valdes 19 Sep '11

19 Sep '11

Here are two changes (reductions) in requested allocations, one for a new project and the other for a renewal. Apparently they didn't want to be a part of the 1M club (ie, give a presentation, as they said they are tied up with other work at the moment). Any objections to reducing these requests to the amounts given below? Comp_Nanocatalysis is a renewal which originally asked for 1.2M Comp_Soft_Catalysts is a new project which originally asked for 1M. John ----- Forwarded message from "Lopez-Encarnacion, Juan Manuel" <JMLopez(a)anl.gov> ----- Date: Mon, 19 Sep 2011 16:15:41 -0500 From: "Lopez-Encarnacion, Juan Manuel" <JMLopez(a)anl.gov> To: support(a)lcrc.anl.gov Cc: jellinek(a)anl.gov Subject: [lcrc-support #87491] Change on allocation time requested Reply-To: support(a)lcrc.anl.gov, "Lopez-Encarnacion, Juan Manuel" <JMLopez(a)anl.gov> Dear Team, Please, can you change our allocation time requested to the new numbers on right in the proposals: 1. Comp_Nanocatalysis (PI: Julius Jellinek) - 998,000 2. Comp_Soft_Catalysts (PI: Juan M. Lopez-Encarnacion) - 980,000 We understand that with these request not presentation is needed. Please, send us an E-mail confirming this change. Thank you, Juan and Julius ----- End forwarded message -----

1 0

Re: [allocations-admins] [LCRC Accounts] Project Request: STability_Nek
by John Valdes 19 Sep '11

19 Sep '11

FYI, Elia has withdrawn this project request: Date: Mon, 19 Sep 2011 16:22:31 -0500 From: "Merzari, Elia" <emerzari(a)anl.gov> To: "support(a)lcrc.anl.gov" <support(a)lcrc.anl.gov> Could you remove the project ? It was not funded by the LDRD. Elia On Wed, Sep 14, 2011 at 02:17:01PM -0500, accounts(a)lcrc.anl.gov wrote: > 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: Elia Merzari > Applicant's institution: ANL > Applicant's division: NE, MCS > Project Name: STability_Nek > Project title: Development of SPectral element stability analisys tool > Associated funding: LDRD > Other Systems: > Science: To develop a global linear stability analisys code using the Nek5000 framework. > > The tool suggested can be applied to the analysis of virtually any flow system. Applications involving laminar flows would benefit in particular (e.g., microfluidics, biological flows, buoyancy driven flows) since the identification a priori of the Laminar-Turbulent transition threshold would allow for important design considerations (e.g., in the laminar regime heat transfer is dramatically reduced and this should be taken into account). > > However the main application of the proposed methodology would be to the identification of geometrical elements that generate unstable modes. This capability would useful for both turbulent and laminar flows. Coupled with the non-linear solver already present in Nek500 to verify the results, this can lead to : > 1. the removal of expensive instabilities, that are often associated to thermal striping for instance, > 2. the control of turbulent processes; > 3. the control of buoyancy-driven phenomena, which are prone to instabilities. > > > The work would be mainly numerical and theoretical in nature, with the development, verification and validation of the methodology on some relevant test cases. > > Once the methodology in place we plan to test it on some typical benchmark case such as the solution of the stability problem in square channels in 2D and 3D, analyzing the requirement on the spectral discretization. The 2D stability problem for square channels will be delivered at the end of the first year. > > At the same time several 2D test runs will be attempted. > Project description: The Navier-stokes equation for incompressible fluids (with the Boussinesq approximation for the buoyancy term) and the energy equation would be solved through Nek5000 to obtain a steady state. Then the Navier-Stokes equations would be linearized by substituting to each variable the steady state and a superposed Ansatz. > > By neglecting the higher order terms, the Navier stokes equations can be reduced to a generalized complex eigenvalue problem. > > The eigenvalues of the linearized operator wuold then be computed through an Arnoldi algorithm. > The size of the eigenvalue is large since it scales with (N^2), N being the size of the mesh. > > Calculations will be largely parallel, only a small portions of calculations will be non-parallel, corresponding to approximately 5%, due mostly to testing. > > Parallel eigenvalue solvers will be imported/implemented/developed in Nek5000. Nek5000 has excellent scalability proven on both Fusion and BG/P. > > The following tasks have been identified: > > 1) development of the 2D methodology; (50,000-100,000 core-hours). > 2) test with 2D channel cases (100,000-200,000 core-hours) and 2D cavity problems. > 3) test preliminary 3D cases (100,000-200,000 core-hours). > > The use of the LCRC cluster wuold be essential to achieve the goals of the project. > > > Project URL: > Requested allocation: 400000 > Q1: 40000 > Q2: 160000 > Q3: 100000 > Q4: 100000 > Justification: > > > The requester has used undetermined amount 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 > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lists.lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0

[LCRC Accounts] Project Request: anl-dcc
by accounts＠lcrc.anl.gov 19 Sep '11

19 Sep '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: Tsung-Shung Lee Applicant's institution: ANL Applicant's division: Physics Project Name: anl-dcc Project title: Dynamical coupled-channel analysis of hadrons at Argonne Associated funding: DOE Other Systems: NERSC Science: This project will develop theoretical approaches for studying the spectrum and structure of excited nucleons states, and hybird and exotic mesons within the fundamental theory of strong interaction; Quantum Chromodynamics. The results will provide information for advancing our understanding of strong interactions and structure of visible matter in universe. This is part of ANL's effort to achieve a DOE milestone HP7 by 2013. Project description: The computations involve solving a large set of coupled-channel integral equations and searching for parameters to fit the world data of meson production of pion-nucleon and photon-nucleon reactions. The calculations account for eight meson-baryon channels and cover energies up to invariant mass W= 3 GeV. Large complex-matrix (1000 by 1000) need to be inverted many times in chi**2-fit to very extensive data (about 100,000 data points) . Standard fortran codes have been developed to perform parallel computation with Fusion. The codes have been well tested and have performed very well at Fusion and NERSC in the past two years . The project will have 4 members Project URL: Requested allocation: 400000 Q1: 200000 Q2: 100000 Q3: 50000 Q4: 50000 Justification: The requester has used undetermined amount 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

1 0