wiki:BriefOverview

Brief Overview of DMD programs

  • This is described for the linux implementation.
  • The programs are assumed to be in PATH
  • 1HEL.pdb is our example pdb
  • The prompt is $

Preliminary

The program requires the input PDB is CLEAN in the sense that:

  • Individual chain are continuous (no broken chain). If there is a chain break, one needs to insert a "TER" in-between to treat it as two chains.
  • HETATM records including waters can be modeled, which requires additional parameters that are not included by default.
  • The SSBOND section of the PDB is ignored, these are determined by findSS below.

Identify the disulfide Bonds

The findSS program finds the disulfide bonds in a PDB.

usage: findSS complexPDB > inputConstr

Inputs:

  • complexPDB : the prepared PDB file which can contain multiple chains

Outputs:

Example usage:

$ findSS.linux 1HEL.pdb > inputConstr

Create input files for DMD simulation

The complex program prepares the files for the DMD simulation run.

usage: complex paramDir complexPDB newTopParamList Dimension outParam outState fmt

Inputs:

  • paramDir : which contains the topology and parameters
  • complexPDB : the prepared PDB file which can contain multiple chains
  • newTopParamList : contains the list of topology/parameter files for the hetatoms in the PDB.
    • If there are no such atoms in the PDB, one can use either an empty file or "/dev/null" (only for linux).
  • Dimension : defines the size of the simulation box. Format x,y,z or d Do not leave spaces in between. If only one number is assigned, it is cubic box.
  • inConstraints : input constraints

Outputs:

Example usage:

$ complex.linux ../param/ 1hel.pdb /dev/null 500 1HEL.param 1HEL.state inputConstr 1HEL.const

Relaxation

The xDMD program is run separately for relaxation and simultation. This entry describes its usage for relaxation. This step rapidly resolves severe clashes.

usage: xDMD -p paramFile -s stateFile -t txtFile -i taskFile -c constraintFile [-1]

Inputs:

  • paramFile : the parameter file produced by complex
  • stateFile : state or restart file
  • ?? txtFile : the text file. ONLY ONE of txtFile or (paramFile+stateFile) is REQUIRED
  • taskFile : defines the temperature, the thermostat parameter, and the length of the simulation.
    • The temperature unit is kcal/mol/kB. For example, 0.6 in DMD is approximiately 300 Kelvin.
    • The time unit is approximately 50fs.
  • constraintFile : the user-defined constraint file, Optional. Produced by complex.
  • ?? oneBeadHB (-1) : optional

Outputs:

  • relax.dmd_restart : restart file
  • relax.dmd_echo : a file that lists the output parameters
    • Time, temperature, pressure, average & instantaneous potential energy, and instanteous kinetic energy
    • Filename is defined in taskFile
  • relax.dmd_movie : a trajectory file that can be used to produce a sequence of PDBs complex_M2P

Example usage:

 $ xDMD.linux -p 1HEL.param -s 1HEL.state -c 1HEL.const -i relax.task

Production

The xDMD program is run separately for relaxation and simultation. This entry describes its usage for simulation. Here, the input restart (state) file is the restart file from the previous step. the equi.task (or the relax.task) from the previous step also defines how often to save the snapshots (movie files).

usage : xDMD -p paramFile -s relax.dmd_restart -c constraintFile -i taskFile

Inputs:

  • paramFile : the parameter file produced by complex
  • relax.dmd_restart : produced from the relaxation run
  • constraintFile : the user-defined constraint file, Optional. Produced by complex.
  • taskFile : defines the temperature, the thermostat parameter, and the length of the simulation.
    • The temperature unit is kcal/mol/kB. For example, 0.6 in DMD is approximiately 300 Kelvin.
    • The time unit is approximately 50fs.

Outputs:

  • equi.dmd_restart : restart file
  • equi.dmd_echo : a file that lists the output parameters
    • Time, temperature, pressure, average & instantaneous potential energy, and instanteous kinetic energy
    • Filename is defined in taskFile
  • equi.dmd_movie : a trajectory file that can be used to produce a sequence of PDBs complex_M2P

Example usage:

 $ xDMD.linux -p 1HEL.param -s relax.dmd_restart -c 1HEL.const -i equi.task

Generate the PDBs from the movie

complex_M2P reads the dmd_movie file and produces a sequence of PDBs in a file.

usage: complex_M2P paramDir complexPDB newTopParamList movie outPDB [startFrame [nFrames [dFrames]]]

Inputs:

  • paramDir : which contains the topology and parameters
  • complexPDB : the prepared PDB file which can contain multiple chains
  • newTopParamList : contains the list of topology/parameter files for the hetatoms in the PDB
    • If there are no such atoms in the PDB, one can use either an empty file or "/dev/null" (only for linux).
  • movie : the trajectory file
    • e.g. equi.dmd_movie or relax.dmd_movie
  • startFrame : integer defining beginning frame number
  • nFrames : integer defining number of frames
  • dFrames : integer defining frame skip delta

Outputs:

  • outPDB : a PDB output file containing all the movie snapshots separated by 'ENDMDL'

Example usage:

 $ complex_M2P.linux ../param/ 1hel.pdb /dev/null equi.dmd_movie equi.pdbs
Last modified 8 years ago Last modified on Nov 11, 2010 2:50:32 PM