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