diff --git a/doc/Section_history.html b/doc/Section_history.html index a8cad8ada6..5272e34c21 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -31,11 +31,10 @@ GranFlow for granular materials. are being worked on; some haven't been implemented because of lack of time or interest; others are just a lot of work!

-

Creation of atoms:

@@ -155,13 +155,13 @@ commands)
  • orthogonal or non-orthogonal (triclinic symmetry) simulation domains
  • constant NVE, NVT, NPT, NPH integrators
  • thermostatting options for groups and geometric regions of atoms -
  • pressure control via Nose/Hoover barostatting in 1 to 3 dimensions +
  • pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
  • simulation box deformation (tensile and shear)
  • harmonic (umbrella) constraint forces
  • independent or coupled rigid body integration
  • SHAKE bond and angle constraints
  • walls of various kinds -
  • targeted molecular dynamics (TMD) constraints +
  • targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints
  • non-equilibrium molecular dynamics (NEMD)
  • variety of additional boundary conditions and constraints @@ -455,6 +455,12 @@ the list.
    + + + + + + diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index cfba53f6d7..5ff97a316e 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -136,7 +136,7 @@ commands) implicit solvent potentials: hydrodynamic lubrication, Debye long-range Coulombics and dispersion: Ewald, \ PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones - CHARMM, AMBER, OPLS force-field compatibility :ul + CHARMM, AMBER, OPLS, GROMACS, force-field compatibility :ul Creation of atoms: :h4 ("read_data"_read_data.html, "lattice"_lattice.html, @@ -155,13 +155,13 @@ Ensembles, constraints, and boundary conditions: :h4 orthogonal or non-orthogonal (triclinic symmetry) simulation domains constant NVE, NVT, NPT, NPH integrators thermostatting options for groups and geometric regions of atoms - pressure control via Nose/Hoover barostatting in 1 to 3 dimensions + pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions simulation box deformation (tensile and shear) harmonic (umbrella) constraint forces independent or coupled rigid body integration SHAKE bond and angle constraints walls of various kinds - targeted molecular dynamics (TMD) constraints + targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints non-equilibrium molecular dynamics (NEMD) variety of additional boundary conditions and constraints :ul @@ -441,6 +441,12 @@ the list. :link(sjp,http://www.cs.sandia.gov/~sjplimp) +fix smd for steered MD : Axel Kohlmeyer (U Penn) +GROMACS pair potentials : Mark Stevens (Sandia) +lmp2vmd tool : Axel Kohlmeyer (U Penn) +compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U) +CG-CMM user package for coarse-graining : Axel Kohlmeyer (U Penn) +cosine/delta angle potential : Axel Kohlmeyer (U Penn) VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain pair lubricate : Randy Schunk (Sandia) compute ackland/atom : Gerolf Zeigenhain
    fix smd for steered MD Axel Kohlmeyer (U Penn)
    GROMACS pair potentials Mark Stevens (Sandia)
    lmp2vmd tool Axel Kohlmeyer (U Penn)
    compute group/group Naveen Michaud-Agrawal (Johns Hopkins U)
    CG-CMM user package for coarse-graining Axel Kohlmeyer (U Penn)
    cosine/delta angle potential Axel Kohlmeyer (U Penn)
    VIM editor add-ons for LAMMPS input scripts Gerolf Ziegenhain
    pair lubricate Randy Schunk (Sandia)
    compute ackland/atom Gerolf Zeigenhain