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Subsections
General parameters and input/output files
The structure of a typical collective variables calculation is
depicted in Figure 6. Each colvar is a
combination of one or more components (see 9.2),
which are functions of several atomic coordinates. Multiple biasing
or analysis methods can be applied to the same colvars. But care
should be taken that certain methods (such as free energy
reconstruction) do not function properly if other biases are adding
forces to their colvars.
Figure 6:
Example of a collective variables (colvar) configuration.
The colvar ``
'' is defined as the difference between two
distances, each calculated between the centers of mass of two
atom groups. The second colvar ``
'' holds the coordination
number (i.e. the number of contacts) within a radius of 6 Å
between two groups. The third colvar ``alpha'' measures the
degree of
-helicity of the protein segment between
residues 1 and 10. A moving harmonic restraint is applied to the
colvars ``
'' and ``
'', each rescaled by means of width
parameters
and
; the centers of the restraint,
and
, evolve with the simulation time
. The
histogram of ``alpha'' and ``
'' is also recorded on-the-fly.
|
To enable a colvar calculation, the NAMD configuration file must
set two parameters (three when restarting a previous run):
Othe parameters defining a collective variables calculation are not
read from the NAMD configuration file, but from a separate file. As a
consequence, keywords described in the following sections
are not NAMD keywords.
By default, the collective variables module writes three output
files:
Other output files can written by specific methods applied to the
colvars (e.g. by the ABF method, see 9.3.1, or the
metadynamics method, see 9.3.2): as for the colvar
trajectory file, they are meant for analyzing rather than continuing a
simulation. All such files begin with the prefix
outputName
.
Figure 7 shows a typical collective variables
configuration file. Its syntax is similar to that of the
NAMD configuration file (2.2.1), with a few
differences:
- the `=' sign between a keyword and its value,
deprecated in the NAMD config, is not allowed in the colvars config
(i.e. only `keyword value' is valid, and not
`keyword = value');
- Tcl commands and syntax are not allowed;
- for keywords with a boolean value, in addition to the values
yes|on|true and no|off|false, the keyword without
any value evaluates as `on'.
Figure 7:
A typical colvars configuration file
 |
Options like globalOption define general features of the
colvars module, and are described in the following. The options for
the colvar blocks are documented in 9.2, and
those for the colvar biases' blocks biastype1,
biastype2, ...in 9.3.
- colvarsTrajFrequency
(global) Colvar value trajectory frequency
Acceptable Values: positive integer
Default Value: 1
Description: The values of each colvar (and any additional quantities which
have been set to be reported) are written at this frequency to the
file <outputName>.colvars.traj. If the value is
0, the trajectory file is not written. For optimization,
the output is buffered (as is the NAMD log output in most
operating systems), but it is synchronized with the disks every
time the restart file is written.
- trajAppend
(global) Append to trajectory file
Acceptable Values: boolean
Default Value: off
Description: If this flag is enabled, and a file with the same name as the
trajectory file is already present, new data is appended to
that file. Otherwise, a new file is created.
- colvarsRestartFrequency
(global) Colvar module restart frequency
Acceptable Values: positive integer
Default Value: restartFreq
Description: Allows to choose a different restart frequency for the collective
variables module. Redefining it may be useful to trace the time
evolution of those few properties which are not written to the
trajectory file for reasons of disk space.
- analysis
(global) Turn on analysis calculations
Acceptable Values: boolean
Default Value: off
Description: If this flag is enabled, the analysis mode is turned on, and all
the colvars and biasing methods are instructed to perform whatever
analysis they are configured to.
- readTrajectory
(global, analysis mode) Trajectory file to read
Acceptable Values: UNIX filename
Description: If analysis is on, and the colvar module has been
compiled as standalone, the values of the colvars is
read from this file, as if a regular simulation was going on. The
same configuration as that of the run which produced the trajectory should
be used to ensure that data is read properly.
- readBegin
(global, analysis mode) Only read frames from this step
Acceptable Values: positive integer
Default Value: 0
Description: If readTrajectory is defined, only lines starting from
this step number are actually loaded by the colvars.
- readEnd
(global, analysis mode) Only read frames up to this step
Acceptable Values: positive integer
Default Value: 0
Description: If readTrajectory is defined, and this number is larger
than readBegin, only lines up to and including this
step number are actually loaded in the colvars.
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