General setup: Difference between revisions

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Navigation: [[Documentation]] / [[Control file]] / [[General setup]] __NOEDITSECTION__
Navigation: [[Documentation]] / [[Control file]] / [[General setup]]
__NOEDITSECTION__
----
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<div style="float:right;">__TOC__</div>
<div style="float:right;">__TOC__</div>
The general setup of PMFLib can be controlled through the following sections in the {PMFLIB} group. These sections control the behaviour of the PMFLib core ([[#.5Bcontrol.5D|<nowiki>[control]</nowiki>]]), define the units used for input/output data specification ([[#.5Bunits.5D|<nowiki>[units]</nowiki>]]), and the names of input and output files ([[#.5Bfiles.5D|<nowiki>[files]</nowiki>]]).
The general setup of PMFLib can be controlled through the following sections in the {PMFLIB} group. These sections control the behaviour of the PMFLib core ([[#.5Bcontrol.5D|<nowiki>[control]</nowiki>]]), define the units used for input/output data specification ([[#.5Bunits.5D|<nowiki>[units]</nowiki>]]), and specify the names of input and output files ([[#.5Bfiles.5D|<nowiki>[files]</nowiki>]]).


==[control]==
==[control]==
Line 14: Line 15:
| system topology
| system topology
| [[Control key types|string]]
| [[Control key types|string]]
| The name of file with a system topology in AMBER7 format. If provided the loaded topology will be used during ASL masks processing instead of the system topology.
| Specifies the name of a file with the system topology in AMBER7 format. If provided, the loaded topology is used during ASL mask processing instead of the system topology.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fdebug
| fdebug
| off
| off
| [[Control key types|logical]]
| [[Control key types|logical]]
| If enabled it prints debugging information if they are available.
| If enabled, prints debugging information if available.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fprint_masks
| fprint_masks
| off
| off
| [[Control key types|logical]]
| [[Control key types|logical]]
| If enabled it prints detailed information about atoms in each ASL masks.
| If enabled, prints detailed information about atoms in each ASL mask.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fprint_inpcrds
| fprint_inpcrds
| off
| off
| [[Control key types|logical]]
| [[Control key types|logical]]
| If enabled it prints input coordinates inluding atom and residues names and indexes.
| If enabled, prints input coordinates, including atom and residue names and indexes.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fenable_pbc
| fenable_pbc
| off
| off
| [[Control key types|logical]]
| [[Control key types|logical]]
| If enabled then the periodic boundary conditions are used whenever possible. Please note that not all collective variables are influenced by this option.
| If enabled, periodic boundary conditions are used whenever possible. Please note that not all collective variables are influenced by this option.
|}
|}


Line 47: Line 48:
| g/mol
| g/mol
| [[Control key types|string]]
| [[Control key types|string]]
| Unit of molar mass.<br/>Allowed values are: au, a.u., g/mol, amu
| Specifies the unit of molar mass.<br/>Allowed values are: au, a.u., g/mol, amu
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| time
| time
| fs
| fs
| [[Control key types|string]]
| [[Control key types|string]]
| Unit of time.<br/>Allowed values are: au, a.u., fs, ps
| Specifies the unit of time.<br/>Allowed values are: au, a.u., fs, ps
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| length
| length
| A
| A
| [[Control key types|string]]
| [[Control key types|string]]
| Unit of length.<br/>Allowed values are: au, a.u., A, pm, nm
| Specifies the unit of length.<br/>Allowed values are: au, a.u., A, pm, nm
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| angle
| angle
| deg
| deg
| [[Control key types|string]]
| [[Control key types|string]]
| Unit of angle.<br/>Allowed values are: rad, deg
| Specifies the unit of angle.<br/>Allowed values are: rad, deg
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| energy
| energy
| kcal/mol
| kcal/mol
| [[Control key types|string]]
| [[Control key types|string]]
| Unit of energy.<br/>Allowed values are: au, a.u., eV, kcal/mol, kJ/mol
| Specifies the unit of energy.<br/>Allowed values are: au, a.u., eV, kcal/mol, kJ/mol
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| temperature
| temperature
| K
| K
| [[Control key types|string]]
| [[Control key types|string]]
| Unit of temperature.<br/>Allowed values are: K
| Specifies the unit of temperature.<br/>Allowed values are: K
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| pressure
| pressure
| Pa
| Pa
| [[Control key types|string]]
| [[Control key types|string]]
| Unit of pressure.<br/>Allowed values are: Pa, kPa
| Specifies the unit of pressure.<br/>Allowed values are: Pa, kPa
|}
|}


Line 94: Line 95:
| {CVS}
| {CVS}
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies either a PRMFile group or the name of a file containing the collective variable specification.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fpathsdef
| fpathsdef
| {PATHS}
| {PATHS}
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies either a PRMFile group or the name of a file containing the path specification.
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Adaptive Biasing Force Method]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Adaptive Biasing Force Method]]'''
Line 106: Line 107:
| {ABF}
| {ABF}
| [[Control key types|string]]
| [[Control key types|string]]
| It defines either a PRMFile group or a file name containing the specification of collective variables used by the ABF method.
| Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the ABF method.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fabfmask
| fabfmask
| _abf.mask
| _abf.mask
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the name of the file that contains ABF force weights.
| Specifies the name of the file containing ABF force weights.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fabfout
| fabfout
| _abf.out
| _abf.out
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the file name used as output from ABF method simulations. This file contains status information and the progress of collective variables in time.
| Specifies the file name used for output from ABF simulations. This file contains status information and the progress of collective variables in time.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fabfrst
| fabfrst
| _abf.rst
| _abf.rst
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the name of the file with accumulated results from ABF simulations.
| Specifies the name of the file containing accumulated results from ABF simulations.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fabftrj
| fabftrj
| _abf.trj
| _abf.trj
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the name of the file containing the time evolution of accumulated ABF results.
| Specifies the name of the file containing the time evolution of accumulated ABF results.
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Adaptive Biasing Potential Method]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Adaptive Biasing Potential Method]]'''
Line 133: Line 134:
| {ABP}
| {ABP}
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the ABP method.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fabpout
| fabpout
| _abp.out
| _abp.out
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies the file name used for output from ABP simulations. This file contains status information and the progress of collective variables in time.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fabprst
| fabprst
| _abp.rst
| _abp.rst
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies the name of the file containing accumulated results from ABP simulations.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fabptrj
| fabptrj
| _abp.trj
| _abp.trj
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies the name of the file containing the time evolution of accumulated ABP results.
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Constrained Dynamics]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Constrained Dynamics]]'''
Line 155: Line 156:
| {CST}
| {CST}
| [[Control key types|string]]
| [[Control key types|string]]
| It defines either a PRMFile group or a file name containing the specification of constraints.
| Specifies either a PRMFile group or the name of a file containing the constraint specification.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fcstout
| fcstout
| _cst.out
| _cst.out
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the file name used as output from constrained dynamics simulations. This file contains status information and the progress of the calculation in time.
| Specifies the file name used for output from constrained dynamics simulations. This file contains status information and the progress of the calculation in time.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fcstdump
| fcstdump
| _cst.dump
| _cst.dump
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies the name of the file containing dumped data from constrained dynamics simulations.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fcstrst
| fcstrst
| _cst.rst
| _cst.rst
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the name of the file with results from the constrained dynamics simulation. This file is used for constrained dynamics calculation restarts.
| Specifies the name of the file containing results from constrained dynamics simulations. This file is used for constrained dynamics restarts.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fcsttrj
| fcsttrj
| _cst.trj
| _cst.trj
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies the name of the file containing the time evolution of accumulated constrained dynamics results.
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Restrained Dynamics]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Restrained Dynamics]]'''
Line 182: Line 183:
| {RST}
| {RST}
| [[Control key types|string]]
| [[Control key types|string]]
| It defines either a PRMFile group or a file name containing the specification of restraints used in restrained dynamics simulations.
| Specifies either a PRMFile group or the name of a file containing the specification of restraints used in restrained dynamics simulations.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| frstout
| frstout
| _rst.out
| _rst.out
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the file name used as output from restrained dynamics simulations. This file contains status information and the progress of restrained collective variables in time.
| Specifies the file name used for output from restrained dynamics simulations. This file contains status information and the progress of restrained collective variables in time.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| frsthist
| frsthist
| _rst.hist
| _rst.hist
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the name of the file containing the run-time histogram of collective variables.
| Specifies the name of the file containing the run-time histogram of collective variables.
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Metadynamics]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Metadynamics]]'''
Line 199: Line 200:
| {MTD}
| {MTD}
| [[Control key types|string]]
| [[Control key types|string]]
| It defines either a PRMFile group or a file name containing the specification of metadynamics collective variables.
| Specifies either a PRMFile group or the name of a file containing the specification of metadynamics collective variables.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fmtdout
| fmtdout
| _mtd.out
| _mtd.out
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the file name used as output from the metadynamics method. This file contains status information and the progress of collective coordinates in time.
| Specifies the file name used for output from the metadynamics method. This file contains status information and the progress of collective coordinates in time.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fmtdrst
| fmtdrst
| _mtd.rst
| _mtd.rst
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the name of the file containing accumulated Gaussian hills from metadynamics simulations.
| Specifies the name of the file containing accumulated Gaussian hills from metadynamics simulations.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fmtdtrj
| fmtdtrj
| _mtd.trj
| _mtd.trj
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies the name of the file containing the time evolution of accumulated metadynamics results.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fmtdhills
| fmtdhills
| _mtd.hills
| _mtd.hills
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the name of the file containing accumulated Gaussian hills from metadynamics simulations.
| Specifies the name of the file containing accumulated Gaussian hills from metadynamics simulations.
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[String Method]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[String Method]]'''
Line 226: Line 227:
| {STM}
| {STM}
| [[Control key types|string]]
| [[Control key types|string]]
| It defines either a PRMFile group or a file name containing the specification of collective variables used by the string method.
| Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the string method.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fstmout
| fstmout
| _stm.out
| _stm.out
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the file name used as output from string method simulations.
| Specifies the file name used for output from string method simulations.
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Path Driving]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Path Driving]]'''
Line 238: Line 239:
| {PDRV}
| {PDRV}
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies either a PRMFile group or the name of a file containing the path driving specification.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fpdrvout
| fpdrvout
| _pdrv.out
| _pdrv.out
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies the file name used for output from path driving simulations.
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Collective Variable Monitoring]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Collective Variable Monitoring]]'''
Line 250: Line 251:
| {MON}
| {MON}
| [[Control key types|string]]
| [[Control key types|string]]
| It defines either a PRMFile group or a file name containing the specification of collective variables used during monitoring.
| Specifies either a PRMFile group or the name of a file containing the specification of collective variables used during monitoring.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fmonout
| fmonout
| _mon.out
| _mon.out
| [[Control key types|string]]
| [[Control key types|string]]
| It defines the file name used as output from collective variable monitoring.
| Specifies the file name used for output from collective variable monitoring.
|-
|-
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Metric Tensor Analysis]]'''
| colspan="4" style="text-align: center; background-color: #CCCCFF;" | '''[[Metric Tensor Analysis]]'''
Line 262: Line 263:
| {MTA}
| {MTA}
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by metric tensor analysis.
|- style="vertical-align: top;"
|- style="vertical-align: top;"
| fmtaout
| fmtaout
| _mta.out
| _mta.out
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies the file name used for output from metric tensor analysis.
|- style="vertical-align: top; background-color: #f6f6f6;"
|- style="vertical-align: top; background-color: #f6f6f6;"
| fmtarst
| fmtarst
| _mta.rst
| _mta.rst
| [[Control key types|string]]
| [[Control key types|string]]
|  
| Specifies the name of the file containing accumulated results from metric tensor analysis.
|}
|}

Latest revision as of 09:52, 21 June 2026

Navigation: Documentation / Control file / General setup

The general setup of PMFLib can be controlled through the following sections in the {PMFLIB} group. These sections control the behaviour of the PMFLib core ([control]), define the units used for input/output data specification ([units]), and specify the names of input and output files ([files]).

[control]

Key Default value Type Description
ftopology system topology string Specifies the name of a file with the system topology in AMBER7 format. If provided, the loaded topology is used during ASL mask processing instead of the system topology.
fdebug off logical If enabled, prints debugging information if available.
fprint_masks off logical If enabled, prints detailed information about atoms in each ASL mask.
fprint_inpcrds off logical If enabled, prints input coordinates, including atom and residue names and indexes.
fenable_pbc off logical If enabled, periodic boundary conditions are used whenever possible. Please note that not all collective variables are influenced by this option.

[units]

Key Default value Type Description
mass g/mol string Specifies the unit of molar mass.
Allowed values are: au, a.u., g/mol, amu
time fs string Specifies the unit of time.
Allowed values are: au, a.u., fs, ps
length A string Specifies the unit of length.
Allowed values are: au, a.u., A, pm, nm
angle deg string Specifies the unit of angle.
Allowed values are: rad, deg
energy kcal/mol string Specifies the unit of energy.
Allowed values are: au, a.u., eV, kcal/mol, kJ/mol
temperature K string Specifies the unit of temperature.
Allowed values are: K
pressure Pa string Specifies the unit of pressure.
Allowed values are: Pa, kPa

Units specified in this section are used only for input parameters and for data written to output files. Data written to restart files or other internal files are still stored in internal units.

[files]

Key Default value Type Description
Collective Variables / Paths
fcvsdef {CVS} string Specifies either a PRMFile group or the name of a file containing the collective variable specification.
fpathsdef {PATHS} string Specifies either a PRMFile group or the name of a file containing the path specification.
Adaptive Biasing Force Method
fabfdef {ABF} string Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the ABF method.
fabfmask _abf.mask string Specifies the name of the file containing ABF force weights.
fabfout _abf.out string Specifies the file name used for output from ABF simulations. This file contains status information and the progress of collective variables in time.
fabfrst _abf.rst string Specifies the name of the file containing accumulated results from ABF simulations.
fabftrj _abf.trj string Specifies the name of the file containing the time evolution of accumulated ABF results.
Adaptive Biasing Potential Method
fabpdef {ABP} string Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the ABP method.
fabpout _abp.out string Specifies the file name used for output from ABP simulations. This file contains status information and the progress of collective variables in time.
fabprst _abp.rst string Specifies the name of the file containing accumulated results from ABP simulations.
fabptrj _abp.trj string Specifies the name of the file containing the time evolution of accumulated ABP results.
Constrained Dynamics
fcstdef {CST} string Specifies either a PRMFile group or the name of a file containing the constraint specification.
fcstout _cst.out string Specifies the file name used for output from constrained dynamics simulations. This file contains status information and the progress of the calculation in time.
fcstdump _cst.dump string Specifies the name of the file containing dumped data from constrained dynamics simulations.
fcstrst _cst.rst string Specifies the name of the file containing results from constrained dynamics simulations. This file is used for constrained dynamics restarts.
fcsttrj _cst.trj string Specifies the name of the file containing the time evolution of accumulated constrained dynamics results.
Restrained Dynamics
frstdef {RST} string Specifies either a PRMFile group or the name of a file containing the specification of restraints used in restrained dynamics simulations.
frstout _rst.out string Specifies the file name used for output from restrained dynamics simulations. This file contains status information and the progress of restrained collective variables in time.
frsthist _rst.hist string Specifies the name of the file containing the run-time histogram of collective variables.
Metadynamics
fmtddef {MTD} string Specifies either a PRMFile group or the name of a file containing the specification of metadynamics collective variables.
fmtdout _mtd.out string Specifies the file name used for output from the metadynamics method. This file contains status information and the progress of collective coordinates in time.
fmtdrst _mtd.rst string Specifies the name of the file containing accumulated Gaussian hills from metadynamics simulations.
fmtdtrj _mtd.trj string Specifies the name of the file containing the time evolution of accumulated metadynamics results.
fmtdhills _mtd.hills string Specifies the name of the file containing accumulated Gaussian hills from metadynamics simulations.
String Method
fstmdef {STM} string Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the string method.
fstmout _stm.out string Specifies the file name used for output from string method simulations.
Path Driving
fpdrvdef {PDRV} string Specifies either a PRMFile group or the name of a file containing the path driving specification.
fpdrvout _pdrv.out string Specifies the file name used for output from path driving simulations.
Collective Variable Monitoring
fmondef {MON} string Specifies either a PRMFile group or the name of a file containing the specification of collective variables used during monitoring.
fmonout _mon.out string Specifies the file name used for output from collective variable monitoring.
Metric Tensor Analysis
fmtadef {MTA} string Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by metric tensor analysis.
fmtaout _mta.out string Specifies the file name used for output from metric tensor analysis.
fmtarst _mta.rst string Specifies the name of the file containing accumulated results from metric tensor analysis.
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