Hello, A change in allocation has been requested: Requester: perezsalas (Ursula Perez Salas) Project: lipidmovement Title: Curvature Effect on the Movement of Lipids Within and Between Membranes Description: Earlier, we have used a unilamellar lipid (DPPC) vesicle, 30 nm in diameter, solvated in water consisting of 10 6 coarse-grained particles, to investigate what effect the curvature has on the free energy of lipid flip-flop across the membrane. This size of vesicle is similar to those used in neutron scattering exper- iments to which we compare the results of the simulations. We found that there is indeed a small but noticeable curvature effect on the free energy of DPPC flip-flop. Using vesicles similar to the DPPC model vesicle, we will build several new vesicle systems consisting either of POPS and POPC at two different cholesterol concentrations and use these systems to calculate the free energy for cholesterol flip-flop and desorption to investigate the effect of curvature on charged and uncharged membranes. Specifically, we will investigate each vesicle system at at three different temperatures for cholesterol concentrations, leading to a total of six systems. In order to estimate the rate of direct absorption of cholesterol, we will run a series of small, flat membrane simulations where we place a cholesterol molecule just outside the membrane and let it get absorbed without any external influence. Here we will run a set of 25 small simulations measuring the absorption time per system, with two rate estimations per simulation. To investigate the temperature dependence of the absorption rates we will simulate one POPS-cholesterol system and one POPC-cholesterol system at four different temperatures, yielding a total of 8 simulation sets. To calculate the needed free energy profiles we will use the umbrella sampling technique which is particularly useful when proper sampling can not be reached in a simple long equilibrium simulation. To do this, the system is constrained to sample a small region of phase space with a known external potential added to the system potential. The set of constraints used to sample the systems are independent of each other, which means that Umbrella Sampling simulations can be run in parallel. The output sampling data is combined using the Weighted Histogram Analysis method, post simulation. **Estimate of number of core-hours: Direct absorption simulations in the flat membrane systems: 25 × 8 = 200 simulations are needed. With each simulation running on one node of 8 cores at 24 h/simulation (estimated from a benchmark of 0.0064 days/ns) to get enough data, will yield a need for 200 × 24 × 8 = 38,400 ≈ 40,000 core-hours. Vesicle system equilibration simulations: We need to equilibrate the vesicle systems before using them in the free energy calculations. A typical equilibration time is 300 - 400 ns, which with a benchmark time of 0.007 ns/day yields a need for 48 h per simulation. Run on 512 cores, we would need 48 h/simulation × 6 simulation × 512 cores = 147456 ≈ 150,000 core-hours. Cholesterol flip-flop and desorption free energy sampling in the vesicles: 6 systems × 5 simulations/system = 30 sampling simulations are needed. With 30,000 data points per sam- pling region, collected at every 1 ps as a minimum data requirement and with a benchmark time of 0.06 days/ns, we need 32 h per simulation, but 35 - 40 h is desirable. A vesicle simulation typically 600 cores to run at this pace, which yields 30 simulations × 40 hours/simulation × 600 cores ≈ 720,000 core-hours. In total, we need 40, 000 + 150, 000 + 720, 000 ≈ 910,000 core-hours were the 40,000 core hours for the absorption estimate simulations are used on independently run small simulations. We will use the molecular dynamics program NAMD, which is developed at University of Illinois at Urbana-Champaign and is freely available for download (http://www.ks.uiuc.edu/Research/namd/). NAMD is highly parallel and scales efficiently with the number of particles in the system. With the release of version 2.10 of NAMD we have seen an increase in efficiency of about 15 % on other machines for the proposed vesicle systems. Thus we believe that the obtained core hours could be used more efficiently with the new version of NAMD also on the Blues and Fusion clusters. Benchmarks obtained at the UIC Extreme cluster on a 1M coarse-grained particle system: Cores | 80 | 160 | 240 | NAMD 2.9 | 76.9 ns/day | 108 ns/day | 120.7 ns/day | NAMD 2.10 | 83.3 ns/day | 129.8 ns/day | 138.8 ns/day | Current: undetermined amount Justification: The vesicle systems have an obvious advantage of using the clusters at Argonne, since they need hundreds of cores to reach peak efficiency which is something that is far from feasible even on a high end private desktop computer. Current benchmarks used to estimate the core-hours needed for the vesicle system equilibration simulations are from old scaling tests. We have not yet been able to try the new version of NAMD on the blues cluster, but benchmarks obtained at the UIC Extreme cluster on a 1M coarse-grained particle system shows a good scaling up to at least 240 cores and a speedup of 10-20 % compared to NAMD 2.9: Cores | 80 | 160 | 240 | NAMD 2.9 | 76.9 ns/day | 108 ns/day | 120.7 ns/day | NAMD 2.10 | 83.3 ns/day | 129.8 ns/day | 138.8 ns/day | The obvious bottleneck in our project is the umbrella sampling of the vesicle systems. The one order of magnitude slowdown that can be seen when comparing the benchmark numbers between the equilibrium simulations with the umbrella sampling simulations is due to the fact that the force calculations needed for the external constraints applied to the systems during sampling cannot be run in parallel. However, the code used to apply the constraints is user made and we plan on revising e.g. the update frequency of the lists needed to perform the force calculations and the output frequency of our sampled variables. Requested: 30000 A specific reason has been given: Our work has required the usage of all our current allocated simulation time on half the time estimated. We are very close to having a publication and the last of our simulations are critical for finishing our analysis. Given our current usage and the simulations needed to finish the analysis, we ask for 30 000 more core hours to be added to our current allocation. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System