NAME

mimesis - three-dimensional molecular mechanics

SYNOPSIS

mimesis -d desfile -ai[ n ] inarcfile -ao outarcfile [ options ]

mimesis -d desfile -a arcfile [ options ]

DESCRIPTION

In the first form of the command, the first (or n-th if specified or last if n is specified to be 0) record of the binary archive file inarcfile is read as the starting coordinates and/or velocities for the simulation with the binary descriptor file desfile and any subsequent archive commands within the simulation will cause coordinates and/or velocities to be written to the binary archive file outarcfile. desfile and inarcfile must contain the same number of atoms.

In the second form of the command, the last record of the binary archive file arcfile is used as a starting point for the simulation with the binary descriptor file desfile and subsequent archives will be appended to the same archive file arcfile. desfile and arcfile must contain the same number of atoms.

In both cases, the path of the simulation is driven by Yammp Shell commands which are read from the standard input and the progress of the simulation is written to the standard output and diagnostics are written to the standard error output.

The options are:

-n N_atom specifies N_atom atoms in the system. This is not necessary as the number of atoms is specified in both the descriptor and archive files. If specified, this must match the number of atoms in both the descriptor and archive files.

-s ysh specifies that the commands will be read from the file ysh instead of from the standard input. This is a convenience feature for VMS systems where there is no simple syntax to redirect a file to the standard input on the mimesis command line.

-p ymp specifies the name of a yammp function definition file ymp which is used in a MD-CONTRA simulation. The source language is FORTH based and the programs are compiled by ympf to the instructions of the mimesis virtual machine.

-o obj specifies the name of a compiled script file obj. This cannot be specified along with -s. This feature is deprecated, and there is no longer a way to generate a compiled script file anyway.

EXAMPLE

mimesis -d dna.ds -a dna.ar < minim.ysh > dna.out

Run a mimesis simulation with the descriptor file dna.ds using the last record of the archive file dna.ar as starting coordinates and appending resulting coordinates to the same archive file. The instructions for the simulation were previously prepared and saved in the file minim.ysh and this is read in from the standard input for the simulation and the progress of the simulation is saved in the file dna.out. (Note the diagnostics which are written to the standard error output are not saved to dna.out.)

mimesis -d rna.ds -ai5 rna-start.ar -ao rna.ar

Run a mimesis simulation with the descriptor file rna.ds using the 5-th record of the archive file rna-start.ar as starting coordinates and writing the subsequent archives to the file rna.ar. The commands are taken from the standard input and the progress of the simulation is written to the standard output.

FILES

SEE ALSO

The Yammp Shell, the descriptor file format, the archive file format, mimesis diagnostics, arc and des, ympf.

DIAGNOSTICS

The standard output and the standard error output are numbered on the same sequence. If the two outputs are separated (for example if the standard output is redirected to a file while the standard error is not) the simulation sequence can still be traced through the two outputs.

The diagnostics for mimesis are quite extensive and documented on a separate page.

BUGS

There is no protection against numerical overflows and (futile) calculations will continue with the overflow. However, there should not be any memory access violations provided descriptors have been checked with des and passed all level 1 checks.

NOTES