2.2. DATAS#
2.2.1. MD Analysis#
The DATAS module performs graphical and statistical analysis of simulated properties, through a unified interface for the ORCA and GROMACS programs. The module can be run from the main program or directly from the command:
datas ⟨simbox.ext⟩ [⟨-options⟩]
where ext is one of the extensions recognized by Solvate Suite (out [ORCA], or log [GROMACS]), and “-options” a set of the configurations for the simulation execution.
Note
Simply type datas in the terminal and press enter to see the full list of execution options for the module.
To assess the equilibrium, the properties acquired during the simulation can be analyzed with the following basic command structure:
datas ⟨simbox.ext⟩
Properties such as pressure, temperature, density, and potential energy are evaluated graphically and statistically (descriptive statistics include the calculation of standard error, standard deviation and drift of properties; RMSD and RDF analysis are also available).
After a production step, simulation data extraction can be performed with trajectory truncation. Several options are available, including the ability to perform RMSD and RDF analyses of the truncated trajectory. The simplest procedure is to run the command:
datas ⟨simbox.ext⟩ -ext
It is possible to apply a set of filters to the extraction of configurations. For example, it is possible to extract configurations whose pressure is around the target pressure P, within a narrow window of ±D:
datas ⟨simbox.ext⟩ -ext -ptr [P:D]
2.2.2. DATAS Options#
datas ⟨file.ext⟩ [-dat [-opt]][-plt [-opt]] [-trj [-opt]]
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auto : Execute an automated properties extraction from simulation files. [-da](●)(■)
» Description
Properties extraction + statistical and graphical analysis
» NOTE: this option is recommended in queue systems.
+ ----------------------------------------------------------
-dat : Generate a dat file only. [for GMX: -min|-opt|-nvt|-npt] [-df](●)(■)
-cpt : Generate a dat file in compact format. [-cp](●)(■)
-dot : Convert dots to commas. [-dt](●)(■)
-psa : Performs statistical analysis. [-ps](●)(■)
-for : Force new property data extraction. [-fm](●)(■)
+ ----------------------------------------------------------
-rms : RMSD analysis for SLT molecular residue (full trajectory). [-rs] (■)
-rdf : RDF analysis for center of masses of ref SLT and sel SVT residues. [-rd] (■)⁽†⁾
= [I:J] : RDF analysis for ref SLT/I and sel SVT/J labels. [-rd] (■)
-pdf : PDF analysis for center of masses of ref SLT and sel SVT residues. [-pd](●)(■)⁽‡⁾
= [I:J] : PDF analysis for ref SLT/I and sel SVT/J indexes. [-pd](●)(■)
-sma : Calculate simple moving average at frequency 5 to the extracted RDF data. [-sm] (■)
-tim = Final simulation interval (in ps) to extract RDF data (def.: 100 ps). [-tm] (■)
-cnv = Cumulative numerical value to be highlighted in the RDF/PDF analysis. [-cv](●)(■)
-shw : Visualize the performed SMA analysis. [-sh] (■)
+ ----------------------------------------------------------
-plt : Generate graphs for params vs simulation time. [-pl](●)(■)
-stp : Generate graphs for params vs simulation step. [-st](●)(■)
+ ----------------------------------------------------------
-trj : Analize the trajectory file. [-tr](●)(■)
-ext : Extract a truncated trajectory file. [-tr](●)(■)
-ctr = [I:J] : Skip I equilibration steps and extract J production steps. [-ct](●)(■)⁽*⁾
-btr = [B:X] : Select frames from B trajectory blocks into X% final steps. [-bt](●)(■)⁽*⁾
-ptr = [P:D] : Select configurations aroud pressure P with tolerance ±D (in bar). [-pt] (■)⁽*⁾
-prd : Select configuration production steps only and the corresponding properties. [-pr](●)(■)⁽*⁾
-grp : Extrac short-ranged non-bonded potential energies. [-gr] (■)⁽*⁾
-nbx : Do not make corrections for “fragmented” molecules near the box edges. [-nb] (■)
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⁽*⁾ Configurable options in automated mode. (●) ORCA available. (■) GROMACS available.
⁽†⁾ RDF = Radial Distribution Function. (from TRJ.XTC file)
⁽‡⁾ PDF = Pair Distribution Function. (from TRY.XYZ file)
2.2.3. MD Statistics#
The STATS module performs statistical analysis of simulated properties, through a unified interface for the ORCA and GROMACS programs. It can be used from the command:
stats ⟨simbox.ext⟩ [⟨-options⟩]
where ext is one of the extensions recognized by Solvate Suite (out [ORCA], or log [GROMACS]), and “-options” a set of the configurations for the simulation execution.
Note
Simply type stats in the terminal and press enter to see the full list of execution options for the module.
2.2.4. STATS Options#
stats ⟨datafile.dat⟩ [⟨-options⟩]
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-cpt : Read a generated dat file in compact format. [-cp]
-for : Force new property data extraction. [-fm]
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2.2.5. MD Graphics#
The PLOTS module performs graphical analysis of simulated properties, through a unified interface for the ORCA and GROMACS programs. It can be used from the command:
plots ⟨simbox.ext⟩ [⟨-options⟩]
where ext is one of the extensions recognized by Solvate Suite (out [ORCA], or log [GROMACS]), and “-options” a set of the configurations for the simulation execution.
Note
Simply type plots in the terminal and press enter to see the full list of execution options for the module.
2.2.6. PLOTS Options#
plots ⟨inputs.ext⟩ [⟨-options⟩]
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Formatted plots:
+ ----------------------------------------------------------
-tim : Plot graphs for params vs simulation time. [-tm]
-stp : Plot graphs for params vs simulation step. [-st]
-cnv = Cumulative value to be highlighted in RDF analysis. [-cv]
+ ----------------------------------------------------------
General plots:
+ ----------------------------------------------------------
-csv : Load an unformated general plot. [-cs]
-plt : Plot y versus x as lines (default). [-pt]
-sct : A scatter plot of y vs x with varying marker size/color. [-sc]
-bar : Make a bar plot. [-br]
-stm : Create a stem plot. [-st]
+ ----------------------------------------------------------
-sma : Simple moving average to the extracted RDF data. [-sm]
+ ----------------------------------------------------------
Saving plots:
+ ----------------------------------------------------------
-bak : Save generated graphs (without iterative interface). [-bk]
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⁽*⁾ ext = dat, rms, rdf, csv, nmr
2.2.7. MD Trajectories#
The TRAJS module performs the extraction of simulated trajectory from GROMACS program. It can be used from the command:
trajs ⟨simbox.gro⟩ [⟨-options⟩]
Note
Simply type trajs in the terminal and press enter to see the full list of execution options for the module.
2.2.8. TRAJS Options#
trajs ⟨trajectory.gro/xtc⟩ [⟨-options⟩]
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auto : Execute an automated trajectory extraction from simulation files. [-ta](●)(■)
» Description
btrj = 1000 blocks with 10% extraction
» NOTE: this option is recommended in queue systems.
+ #1: Individual Options - (no data analysis) ------------------------------
-itr = I : Extracts position structure #I from the trajectory. [-it](●)(■)⁽†⁾
-ntr = N : Extract N equaly spaced MD steps for truncated trajectory. [-nt](●)(■)
-str = M : Extract equaly spaced frames at every M steps from trajectory. [-st](●)(■)
+ #2: Combinable Options - (with data analysis) ----------------------------
-ctr = [I:J] : Skip I equilibration steps and extract J production steps. [-ct](●)(■)⁽*⁾
-btr = [B:X] : Select frames from B trajectory blocks into X% final steps. [-bt] (■)⁽*⁾
-ptr = [P:D] : Select configurations around pressure P with tolerance ±D (in bar). [-pt] (■)⁽*⁾
+ #3: Output file formats - (GROMACS only) ---------------------------------
-xyz : Output in XYZ file format. [default] [-xy] (■)
-pdb : Output in PDB file format. [-pd] (■)
-gro : Output in GRO file format. [-gr] (■)
+ #4: Other Options --------------------------------------------------------
-prd : Select configuration production steps only and the corresponding properties. [-pr](●)(■)⁽*⁾
-grp : Extract short-ranged non-bonded potential energies. [-gr] (■)⁽*⁾
-nbx : Don´t make corrections for “fragmented” molecules near the box edges. [-nb] (■)
-bak : Save intermediate PDB and XVG files for alternative convertions. [-bk] (■)
-deb : Save intermediate XVG file and create a reconstructed ENT file. [-db] (■)
-for : Force new extraction and override previous PDB file. [-fm](●)(■)
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⁽*⁾ Configurable options in automated mode. (●) ORCA available. (■) GROMACS available.
⁽†⁾ Structure position, not configuration step.
2.2.9. Quickstart Examples#
Example #1: Data analysis from ORCA simulation
Example #2: Data analysis from GROMACS simulation