User Manual

Introduction

  • intro - introduction to commands, yammp programs, and molecular simulation.

Programs

Create a force field description for the model (descriptor file)

  • There is no utility to do this for a general model at the moment. There are programs for specific types of models though:
  • mkchaindes - generate a descriptor for a simple RNA model
  • mkd3d - generate descriptor for closed circular 3DNA model
  • mksnad - generate descriptor for ribosomal RNA models.

Create a starting conformation (archive file)

  • There is no general utility. It is simple enough to convert a PDB file to an archive though.
  • mkchainarc - generate a biased random walk chain
  • mkd3c - generate 3DNA coordinates in various trajectories
  • mkr2cc
  • mksnac

Once a descriptor and starting conformations are available, simulation can be carried out.

  • mimesis - molecular simulations in three-dimensions

Results of simulations can be analyzed and perhaps used for further simulations

  • exam - examine yammp archives
  • xmd3 - examine archives of 3DNA models
  • xmr2

There are various utilities to manipulate descriptor and archive files

  • arc - interconvert archive files between internal (binary) and external (text) formats
  • arcedit - edit archive files
  • arctransform - rigid body transformations
  • des - interconvert descriptor files between internal (binary) and external (text) formats
  • elec2vlat - convert electron density to the vector lattice term
  • checkspider - read a spider file and output the values
  • ympf - compile a yammp postfix source file to binary

File Formats

Languages

Diagnostics


des format
arc format
yammp shell
exam commands
intro
arc
arcedit
arctransform
checkspider
des
elec2vlat

exam
mimesis
mkchainarc
mkchaindes
mkd3c
mkd3d
mkr2cc
mksnac
mksnad
xmd3
xmr2
ympf

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