dcd Class Reference

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Detailed Description

Writes simulation snapshots in the DCD format.

Every period time steps a new simulation snapshot is written to the specified file in the DCD file format. DCD only stores particle positions but is decently space efficient and extremely fast to read and write. VMD can load 100's of MiB of trajectory data in mere seconds.

Use in conjunction with dump.mol2 so that VMD has information on the particle names and bond topology.

Due to constraints of the DCD file format, once you stop writing to a file via disable(), you cannot continue writing to the same file, nor can you change the period of the dump at any time. Either of these tasks can be performed by creating a new dump file with the needed settings.

Public Member Functions
def	__init__
	Initialize the dcd writer.
def	disable
	Disables the analyzer.

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Member Function Documentation

def __init__	(		self,
			filename,
			period,
			overwrite = False
	)

Initialize the dcd writer.

Parameters:

	filename	File name to write to
	period	Number of time steps between file dumps
	overwrite	When False, (the default) an existing DCD file will be appended to. When True, an existing DCD file filename will be overwritten.

Examples:

 dump.dcd(filename="trajectory.dcd", period=1000)<br>
 dcd = dump.dcd(filename"data/dump.dcd", period=1000)

Warning:

When you use dump.dcd to append to an existing dcd file

• The period must be the same or the time data in the file will not be consistent.
• dump.dcd will not write out data at time steps that already are present in the dcd file to maintain a consistent timeline

period can be a function: see Variable period specification for details

def disable

(

self

)

[inherited]

Disables the analyzer.

Examples:

 analyzer.disable()

Executing the disable command will remove the analyzer from the system. Any run() command executed after disabling an analyzer will not use that analyzer during the simulation. A disabled analyzer can be re-enabled with enable()

To use this command, you must have saved the analyzer in a variable, as shown in this example:

 analyzer = analyzer.some_analyzer()
 # ... later in the script
 analyzer.disable()