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.

Quick menu:



New @SoftSimu:


Talks, notes & other random thingies

Software:


Cashew - Coarse Approach Simulator for Hydrogen Bonding Effects in Water

Cashew is a molecular dynamics (MD) implementation of the 3D Mercedes-Benz (MB) model for water [Dias et al., J. Chem. Phys. 131 (2009) 054505]. The code is written in Fortran 90. 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 reproduces 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.

Code: Cashew.

Reference: 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 - dynamical systems

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 (codes are in C and Fortran90):

  • Stochastic rotation or the Malvanets-Kapral method: 2D code
  • Basic Lattice Boltzmann code
  • Basic 2D Dissipative Particle Dynamics code

Reference:Novel Methods in Soft Matter Simulations, M. Karttunen, I. Vattulainen, and A. Lukkarinen (Eds.), Springer Lecture Notes in Physics (2004).

DPDmacs

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.

ReptateDPD - DPD reptation simulation code

Please send us an email to get the code [softsimu at gmail.com]

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.

Reference: Reptational dynamics in dissipative particle simulations of polymer melts, Petri Nikunen, Ilpo Vattulainen, Mikko Karttunen, 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 below paper

Download the Mathematica file from here: Mathematica file

Reference: Stencils with isotropic discretisation error for differential operators, Michael Patra and Mikko Karttunen, Numerical Methods for Partial Differential Equations 22, 936-953 (2005).

Parameters and configurations:


Optimized structures of DPE (diphenylethyne) and friends

Optimized structures of DPE (diphenylethyne), Me-DPE and n-PPE (n=1,2,...,10) (MD and DFT) and input files for the VOTCA package for calculating excitation energies.

Download the configurations and parameters here:

Reference: Behnaz Bagheri, Bjoern Baumeier, Mikko Karttunen, submitted [preprint]

CTAB (cetyltrimethylammonium bromide) parameters

CTAB is a cationic surfactant. The parameterizaton is based on quantum chemistry calculations and NPA analysis.

Download the configurations and parameters here:

Reference: Molecular Dynamics Simulations of DPPC/CTAB Monolayers at the Air/Water Interface, Bin Liu, Matthew I. Hoopes, and Mikko Karttunen, J. Phys. Chem. B 118, 11723-11737 (2014). [online]

Prolyl oligopeptidase (POP) PDB structures with inhibitors. X-ray diffraction structures

X-ray diffraction with resolution of 2.00 Å

Download the PDB files here:

  • 4AMY: Prolyl Oligopeptidase from porcine brain with a covalently bound inhibitor IC-1
  • 4AMZ: Prolyl Oligopeptidase from porcine brain with a covalently bound inhibitor IC-2
  • 4AN0: Prolyl Oligopeptidase from porcine brain with a covalently bound inhibitor IC-3
  • 4AN1: Prolyl Oligopeptidase from porcine brain with a covalently bound inhibitor IC-4

Reference: Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase, Karol Kaszuba, Tomasz Róg, Reinis Danne,Peter Canning ,Vilmos Fülöp, Tünde Juhász, Zoltán Szeltner, J.-F. St. Pierre, Arturo García-Horsman, Pekka T. Männistö, Mikko Karttunen, Jyrki Hokkanen, Alex Bunker, Biochimie 94, 1398-1411 (2012).

DOTAP parameters and configurations

Initial/final configurations and DOTAP (dioleoyloxytrimethylammonium propane) parameters. DOTAP is a cationic lipid. As far as we know, these are the only publically available ones.

Download the configurations and parameters here: DOTAP package

Reference: 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.

Download the end configuration from here: bacterial membrane after 100 ns

References:

  1. 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).
  2. 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.

Download parameters: SDS (sodium dodecyl sulfate)

Reference:

  1. 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).

See also:

  1. Video of micelle (SDS) fission
  2. Micelle fission through surface instability and formation of an interdigitating stalk, M. Sammalkorpi, M. Karttunen, M. Haataja, J. Am. Chem. Soc. 130, 17977-17980 (2008).
  3. Ionic surfactant aggregates in saline solutions: Sodium dodecyl sulphate (SDS) in the presence of excess NaCl or CaCl2, M. Sammalkorpi, M. Karttunen, M. Haataja J. Phys. Chem. B 113, 5863-5870 (2009).
  4. Simulations of micellization of sodium hexyl sulfate, M. Sammalkorpi, S. Sanders, A. Panagiotopoulos, M. Karttunen, M. Haataja, J. Phys. Chem. B. 115, 1403-1410 (2011).

Lipid rafts (PC, cholesterol, sphingomyelin (configurations))

The final configurations from our raft simulations will appear here shortly. If you need them in the meantime, please contact me.

Reference: 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).

Parameters for 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.

Download parameters: Fusidic acid

Reference: 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/).

Download parameters: DMTAP parameters

References:

  1. Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study, Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).
  2. 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).
  3. 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).

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/).

Download parameters: DMPC parameters

References: Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study, Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).

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.

Download:

  1. A table containing the simulation times, areas per lipid and error estimates: TablePDB.pdf.
  2. A tar file containing everything
  3. 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).

References: Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study, Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).

128 DMPC lipids and 3655 water molecules after 20 ns at 50 degrees Celsius.

128 DMPC lipids and 3655 water molecules after 20 ns at 50 degrees Celsius.

Area per lipid: 0.656 (+/- 0.008) nm2.

Download: DPPC bilayer after 100 ns

References: Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study, Gurtovenko, Patra, Karttunen, Vattulainen, Biophys. J. 86, 3461-3472 (2004).

128 DPPC lipids and 3655 water molecules after 100 ns

Equilibrated system of 128 DPPC lipids and 3655 water molecules after 100 ns.

Download: DMPC bilayer

128 DPPC lipids and 3655 water molecules after 100 ns. Area per lipid: 0.645 (+/- 0.010) nm2.

References:

  1. 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)
  2. 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).

POPC bilayer: Final configuration after a 30 ns MD simulation. 128 POPC and 3655 waters.

Download: Final configuration after a 30 ns MD Simulation of 128 POPC and 3655 waters.

Area per lipid: (0.658 +/- 0.009) nm2.

References: 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)

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/).

Download: Topology file for a POPG lipid (anionic, charge: -1)

References: 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 membrane: Final configuration: 150 ns MD Simulation of 128 POPGs, 3527 waters and 128 Na+ ions

Download: Final configuration: 150 ns MD Simulation of 128 POPGs, 3527 waters and 128 Na+ ions

Area per lipid: (0.530 +/- 0.006) nm2.

References: 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)

All the radial distribution functions and final configurations (PDB) from our NaCl force field study.

All the radial distribution functions and final configurations (PDB) from our NaCl force field study.

Download: tar package

References: 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)