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GROMACS is one of the most widely used HPC software packages using the Molecular Dynamics (MD) simulation technique. In this work, we quantify GROMACS parallel performance using different configurations, HPC systems, and FFT libraries (FFTW, Intel MKL FFT, and FFT PACK). We break down the cost of each GROMACS computational phase and identify non-scalable stages, such as MPI communication during the 3D FFT computation when using a large number of processes. We show that the Particle-Mesh Ewald phase and the 3D FFT calculation significantly impact the GROMACS performance. Finally, we discuss performance opportunities with a particular interest in developing GROMACS for the FFT calculations.

The widespread interest in phase recognition of lipid membranes has led to the use of different optical techniques to enable differentiation of healthy and not fully functional cells. In this work, we show how the combination of different (non)linear optical methods such as One Photon Absorption (OPA), Two Photon Absorption (TPA) and Second Harmonic Generation (SHG) as well as the study of the fluorescence decay time leads to an enhanced screening of membrane phases using a fluorescent dioctadecyltetramethylindocarbocyanine (DiD) probe. In the current study we consider the pure liquid disordered phases of DOPC (room temperature) and DPPC (323 K), the solid gel phase of DPPC (298 K), and the liquid ordered phase of a 2:1 binary mixture of Sphingomyelin and Cholesterol. By means of extensive hybrid quantum mechanics molecular mechanics calculations and based upon the (non) linear absorption of the embedded probes, it is found that DiD can be used to identify the lipid bilayer phase. The joint TPA and SHG as well as fluorescence analyses qualifies DiD as versatile probe for phase recognition. In particular, the SHG data obtained by means of HyperRayleigh Scattering and by Electric Field Induced Second Harmonic Generation reveal differences in polarization of the probe in the different environments. The TPA results finally confirm the particular location of the probe in between the polar head group region of the 2:1 SM:Chol mixture in the liquid ordered phase., Comment: 33 pages, 4 figures