SoftSimu - Software, simulation parameters, force fields, configurations
Here you can find software, and coordinate, forcefield and topology files that can be freely downloaded and used. For compatibility with molecular simulation software, please see the description with each file. Coordinates are typically give in PDB format.
Disclaimer: These files & software are provided as they are. We do not guarantee or promise that they are free of erros and we do not accept any liability of any kind (standard disclaimers apply). Use them at your own risk. If you find erros, please let us know and we will try to correct them and update the files accordingly.
If you find out that there are missing files or access problems, please let us know. If unsure, please ask us.
A small request - referencing:
The software and other material here is provided as a service to the scientific community. If you publish works based on software or structures provided here, please cite the references as given with each of the files.
At the end of this page we list some other relevant sites which provide downloadable software and coordinates, forcefields and topologies.
Main categories below:
Software
Parameters and configurations: lipid bilyars, ions, etc.
Other phospholipid sites
Other software sites.
...and now to the downloadables:
1. Software:
Cashew (Coarse Approach Simulator for Hydrogen Bonding Effects in Water) is a molecular dynamics (MD) implementation of the modified 3D Mercedes-Benz (MB) model for water [Dias et al., J. Chem. Phys. 131 (2009) 054505]. The code is written in Fortran 90 programming language. The modified 3D Mercedes-Benz model was originally developed due to the need for a coarse-grained water model for studying geometric effects in interactions of water with solutes, polymers, proteins etc. The model also reproduces well some important properties of water, such as melting at a lower temperature under increased pressure. This molecular dynamics implementation was created for studying the dynamical properties of the model. The program is designed for MD simulations of MB water molecules, offering also the possibility to include other atomic particles with simple interactions and constraints. Both a serial and MPI-parallel versions of the program are available. The code is available here: Cashew.
Ref: A molecular dynamics implementation of the 3D Mercedes-Benz water model, T. Hynninen, C. L. Dias, A. Mkrtchyan, V. Heinonen, M. Karttunen, A. S. Foster, T. Ala-Nissila, Computer Physics Communications 183, 363-369 (2011)
DsTool is a program for interactively exporing the dynamics of dynamical systems. It allows you to draw trajectories, to find fixed points or bifurcation points. DsTool was originally written by Mark Myers, Rick Wicklin, Patrick Worfolk and John Guckenheimer. This release improves the installation mechanism and solves some minor bugs.
Software used in our hands-on computer exercises in SoftSimu2002 summer school.
The above web link includes the following codes:
Stochastic rotation or the Malvanets-Kapral method: 2D code.
Basic Lattice Boltzmann code,
Basic 2D Dissipative Particle Dynamics code.
Ref: Novel Methods in Soft Matter Simulations, M. Karttunen, I. Vattulainen, and A. Lukkarinen (Eds.), Springer Lecture Notes in Physics (2004).
DPDmacs simulation code
DPDmacs is a high-speed code for coarse-grained (DPD) molecular dynamics simulations running exclusively on computers that have the SSE and SSE2 extensions. In practise, this means you need to either have a Pentium-4 or an AMD64 (Athlon64 or Opteron). DPDmacs was developed under Linux, it runs in both 32 and 64 bit mode, but it should compile and run also under other operating systems without problems DPDmacs Due to the use of SSE and SSE2, DPDmacs is extremely fast.
DPD reptation simulation code
Please send us an email to get the code [mkarttu at uwo.ca]
Dissipative Particle Dynamics simulation code for systems containg polymers or other chain like molecules (such as lipids and surfactants) which contains an algorithm to control chain crossings. That enables DPD simulations in the reptation regime which is otherwise impossible due to the softness of the DPD potentials.
Ref: Nikunen, Vattulainen, Karttunen, "Reptational dynamics in dissipative particle simulations of polymer melts", Phys. Rev. E. 75, 036713 (2007).
Mathematica file containing the stencils from the paper Stencils with isotropic discretisation error for differential operators
Isotropic stencils: Mathematica file containing the stencils from the paper "Stencils with isotropic discretisation error for differential operators", Michael Patra and Mikko Karttunen, Numerical Methods for Partial Differential Equations 22, 936-953 (2005).
2. Parameters, configurations, force fields:
DPPC
membrane
DOTAP membranes
&
parameters
DOTAP parameters and configurations
Initial configurations and DOTAP parameters. As far as we know, these are the only publically available ones. Will be provided shortly - if you need the them sooner, drop me an email
If you use these parameters or configurations, please cite:
Cationic DMPC/DOTAP Lipid Bilayers: Atomistic Insight for Structure and Dynamics,
Wei Zhao, Andrey A. Gurtovenko, Ilpo Vattulainen, Mikko Karttunen, J. Phys. Chem. B 116, 269-276 (2012)
POPG/POPE mix - bacterial membrane
The end configuration (PDB) from a simulation of a model of bacterial membrane after 100 ns:
96 POPEs, 32 POPGs, and 3623 water molecules. POPG model is the same in the model provided below.
If you use this, please cite:
Role of phosphatidylglycerols in the stability of bacterial membranes, W. Zhao, T. Róg, A.A. Gurtovenko, I. Vattulainen, M. Karttunen, Biochimie 90, 930-938 (2008).
Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions, W. Zhao, T. Rog, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, Biophys. J. 92, 1114-1124 (2007)
SDS (sodium dodecyl sulfate) parameters & initial configuration
Initial configurations Will be provided shortly.
If you use these parameters or configurations, please cite:
Structural properties of ionic detergent aggregates: A large-scale molecular dynamics study of sodium dodecyl sulfate, M. Sammalkorpi, M. Karttunen, M. Haataja, J. Phys. Chem. B 111, 11722-11733 (2007).
Raft configurations
The final configurations from our raft simulations will appear here shortly.
If you use these, please cite: Assessing the nature of lipid raft membranes, P.S. Niemela, S. Ollila, M.T. Hyvonen, Mikko Karttunen, I. Vattulainen. PLoS Computational Biology 3, e34 (2007).
Fusidic acid is a steroid-based antibiotic derived from Fusidium coccineum. It has been used to treat infections with gram-positive Staphylococcus aureus and it is also effective against corynebacteria, nocardia, anaerobes, and gram-negative Neisseria species.
If you use these parameters, please cite:
Interaction of fusidic acid with lipid membranes: Implications to the mechanism of antibiotic activity, E. Falck, J.T. Hautala, M. Karttunen, P.K.J. Kinnunen, M. Patra, H. Saaren-Seppala, I. Vattulainen, S.K. Wiedmer, and J.M. Holopainen, Biophys. J. 91 1787-1799 (2006).
DMTAP topology file dmtap.itp. DMTAP is cationic, charge: +1
Needs lipid.itp (from Peter Tieleman's web site at http://moose.bio.ucalgary.ca/) or one can use Gromacs force-field files (ffgmx*.itp) with incorporated parameters from lipid.itp (available through www.gromacs.org/).
If you use this topology file, please cite Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).
dmpc.itp: Topology file for a DMPC lipid.
Based on Peter Tieleman's DMPC model and needs lipid.itp (from Peter Tieleman's web site at http://moose.bio.ucalgary.ca/) or one can use Gromacs force-field files (ffgmx*.itp) with incorporated parameters from lipid.itp (available through www.gromacs.org/).
If you use this topology file, please cite Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).
DMTAP & DMPC
mixtures
dmtapPDB.tar.gz: Configurations containing mixtures of DMTAP and DMPC.
A tar file of configurations containing mixtures of DMTAP and DMPC. Total of 128 lipids. The number of water molecules varies with DMTAP concentration (pure DMPC: 3655 waters). Temperature: 50 degrees Celsius.
Here is a table containing the simulation times, areas per lipid and error estimates: TablePDB.pdf.
Individual files if you don't want to download the full tar-package. The number in brackets in time in ns:
0.0% (pure DMPC), 6% (20 ns) 16% (22), 25% (22), 31% (20), 39% (20), 50% (30), 63% (25), 75% (22), 89% (25), 100% (pure DMTAP, 24 ns).
Ref: Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).
DMPC
membrane
dmpc128_20ns.pdb.gz
128 DMPC lipids and 3655 water molecules after 20 ns at 50 degrees Celsius.
Area per lipid: 0.656 (+/- 0.008) nm2.
Ref: Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).
DPPC membrane
dppc-128-100.pdb.gz 128 DPPC lipids and 3655 water molecules after 100 ns.
128 DPPC lipids and 3655 water molecules after 100 ns. Area per lipid: 0.645 (+/- 0.010) nm2.
Refs: Patra, Karttunen, Hyvönen, Falck, Lindqvist, Vattulainen, Biophys. J. 84, 3636-3645 (2003) and
Patra, Karttunen, Hyvönen, Falck, and Vattulainen, J. Phys. Chem. B 108, 4485-4494 (2004).
POPC
membrane
popc.pdb: Final configuration after a 30 ns MD Simulation of 128 POPC and 3655 waters.
Area per lipid: (0.658 +/- 0.009) nm^2. .
Ref: "Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions", W. Zhao, T. Rog, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, Biophys. J. 92, 1114-1124 (2007)
popg.itp Topology file for a POPG lipid (anionic, charge: -1).
Needs lipid.itp (from Peter Tieleman's web site at http://moose.bio.ucalgary.ca/) or one can use Gromacs force-field files (ffgmx*.itp) with incorporated parameters from lipid.itp (available through www.gromacs.org/). .
Ref: "Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions", W. Zhao, T. Rog, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, Biophys. J. 92, 1114-1124 (2007)
popg.pdb Final configuration: 150 ns MD Simulation of 128 POPGs, 3527 waters and 128 Na+ ions.
Area per lipid: (0.530 +/- 0.006) nm^2. .
Ref: "Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions", W. Zhao, T. Rog, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, Biophys J. 92, 1114-1124 (2007)
iondata.tar.gz
All the radial distribution functions and final configurations (PDB) from our NaCl force field study.
Ref: 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)
3. Other phospholipids sites [let me know of any others]:
Peter Tieleman's Group: DPPC, DPC, DMPC, POPC, POPE...
Roland Faller's Group: POPA, etc.
4. Other software sites: