SoftSimu - Downloads Zone

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Dr. Mikko Karttunen
Tel: (519) 661-2111 ext. 88790
Fax: (519) 661-3523
Email: mkarttu [at] uwo.ca

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Software, simulation parameters, force fields...

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). If you choose to use them that is 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:

  1. Software
  2. Parameters and configurations: lipid bilyars, ions, etc.
  3. Other phospholipid sites
  4. Other software sites.

...and now to the downloadables:

1. Software:

DSTool

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, Mikko Karttunen, Ilpo Vattulainen, and Ari Lukkarinen (Eds.), Springer Lecture Notes in Physics (2004).

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). [Online]

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). [Online]

2. Parameters, configurations, force fields:

Bacterial membrane: POPG/POPE mix

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). [On-line]

  • "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).
    [Online]

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). [Online]

Raft configurations

The final configurations from our raft simulations will appear here shortly.

If you use these configurations, 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). [Online]

Fusidic acid.

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). [Online]

dmtap.itp: Topology file for a DMTAP lipid (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).

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).

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.

Ref: Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).

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-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.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: Patra and Karttunen, physics/0211059. J. Comp. Chem. 25, 678-689 (2004)

Other phospholipids sites:

Other software sites: