Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes - we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e., communication between CPUs is possible by directly reading from or writing to other CPUs' local memory. It turns out that the particle-mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster.
Configurations containing cationic (charge: +1) DMTAP and DMPC lipids, water and neutralizing ions (when necessary) at 50 C for the following systems: Pure DMPC: 128 lipids (all DMPC, 0 Cl ions) and 3655 waters. File: dmpc128_20ns.pdb 6% DMTAP: 128 lipids (120 DMPC, 8 DMTAP, 8 Cl ions) and 3647 waters. File: tap06_20ns.pdb 16% DMTAP: 128 lipids (108 DMPC, 20 DMTAP, 20 Cl ions) and 3635 waters 25% DMTAP: 128 lipids (96 DMPC, 32 DMTAP, 32 Cl ions) and 3623 waters 31% DMTAP: 128 lipids (88 DMPC, 40 DMTAP, 40 Cl ions) and 3615 waters 39% DMTAP: 128 lipids (78 DMPC, 50 DMTAP, 50 Cl ions) and 3605 waters 50% DMTAP: 128 lipids (64 DMPC, 64 DMTAP, 64 Cl ions) and 3591 waters 63% DMTAP: 128 lipids (48 DMPC, 80 DMTAP, 80 Cl ions) and 3575 waters 75% DMTAP: 128 lipids (32 DMPC, 96 DMTAP, 96 Cl ions) and 3559 waters 89% DMTAP: 128 lipids (14 DMPC, 114 DMTAP, 114 Cl ions) and 3541 waters Pure DMTAP: 128 lipids (all DMTAP, 128 Cl ions) and 3527 waters: File: dmtap128_24ns.pdb Simulation time for each system is shown in the file name. Parameter files are: dmpc.itp and dmtap.itp. The file lipid.itp is also needed (these are Berger lipids). Download lipid.itp from http://wcm.ucalgary.ca/tieleman/downloads The PDF file (TablePDB.pdf ) contains a summary of the systems with area per lipid and error. References: Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study, Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004). Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations, A. A. Gurtovenko, M. Miettinen, M. Karttunen, and I. Vattulainen J. Phys. Chem. B 109, 21126-21134 (2005). Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions, M.S. Miettinen, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, J. Phys. Chem. B 113, 9226-9234 (2009).
The package contains all the radial distribution functions and final configurations (PDB) from our NaCl force field study Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration and structural properties, M. Patra and M. Karttunen, physics/0211059. J. Comp. Chem. 25, 678-689 (2004) .
By means of atomistic molecular dynamics simulations, we study cholesterol-DPPC (dipalmitoyl phosphatidylcholine) bilayers of different composition, from pure DPPC bilayers to a 1:1 mixture of DPPC and cholesterol. The lateral-pressure profiles through the bilayers are computed and separated into contributions from the different components. We find that the pressure inside the bilayer changes qualitatively for cholesterol concentrations of about 20% or higher. The pressure profile then turns from a rather flat shape into an alternating sequence of regions with large positive and negative lateral pressure. The changes in the lateral-pressure profile are so characteristic that specific interaction between cholesterol and molecules such as membrane proteins mediated solely via the lateral-pressure profile might become possible.
Equilibrated system of 128 DPPC lipids and 3655 water molecules after 100 ns. Details: Berger united atom lipids (needs lipid.itp and dppc.itp from Peter Tieleman's web site at http://moose.bio.ucalgary.ca/). Area per lipid: 0.645 (+/- 0.010) nm2. Also available at: http://www.softsimu.net/downloads.shtml References: Major artifacts due to truncating electrostatic interactions, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, Peter Lindqvist, and Ilpo Vattulainen, Biophys. J. 84, 3636-3645 (2003) Lipid bilayers driven to a wrong lane in molecular dynamics simulations by truncation of long-range electrostatic interactions, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, Emma Falck, and Ilpo Vattulainen, J. Phys. Chem. B 108, 4485-4494 (2004).
The package contains all the radial distribution functions and final configurations (PDB) from our NaCl force field study Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration and structural properties, M. Patra and M. Karttunen, physics/0211059. J. Comp. Chem. 25, 678-689 (2004) .
