4. Additional Modules#
4.1. File Management#
4.1.1. OUTIN#
Manipulation of input/output files
outin ⟨file_inp.ext⟩ ⟨file_out.ext⟩ [⟨-options⟩]
-------------------------------------------------------------------------------------------------
FILE FORMATS [-ff]
-------------------------------------------------------------------------------------------------
.ext: com : Gaussian (read/write)[gjf]
inp : ORCA (read/write)
xyz : xTB (read/write)
gro : GROMACS (read/write)
pdb : PDB (read/write)
log : Gaussian (read)
out : ORCA (read)
xtb : xTB (read)
xtc : GROMACS (read)
trj : XYZ/GRO/PDB (read)
+ ----------------------------------------------------------
cpt : Data Comp (write)[Compress calculated data]
dat : Calc Data (write)[Extract calculated data (option: nogeom)]
sup : Supl Data (write)[Extract supplementary data]
sep : Sepa Data (write)[Separate input/output data]
spl : Splt Data (write)[Split input/output data]
div : Divd Data (write)[Divide input/output data]
job : Jobs Exec (write)[Divide input/output jobs]
frq : Calc Frqs (write)[Extract vibrational frequency data]
ifr = Imag Dist (write)[Imaginary mode distortion (factor of distortion)]
+ ----------------------------------------------------------
slt : SLTs Extn (write)[Solute extraction from trajectory frames]
svt : SVTs Extn (write)[Solvent extraction from trajectory frames]
pcf = PChg File (write)[Solvent as point charges][ = Scale factor for atomic charges ]
-------------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------------
CONVERTION OPTIONS [-co]
-------------------------------------------------------------------------------------------------
-key = “List of keywords” (for Gaussian or ORCA). [-kw]
-add = “List of keywords/additional” (for Gaussian). [-ad]
-svt = Include solvent type for implicit (with ALPB or PCM solvation method). [-sv]
-nmr : Include configuration for NMR calculation (for ORCA). [-nm]
+ ----------------------------------------------------------
-itr = Extract structure nº N of a trajectory. [Value: I] [-it](●)(■)
-ntr = Number N of equaly spaced MD steps for truncated trajectory. [Value: I] [-nt](●)(■)
-str = Extract equaly spaced frames at every M steps from trajectory. [Value: I] [-st] (■)
-ctr = Skipe I equilibration and extract J production MD steps (auto mode). [Value: [I:J]] [-ct](●)(■)
-btr = Select frames from I trajectory sections into J% final steps. [Value: [I:J]] [-bt] (■)
-ptr = Select frames aroud pressure P with tolerance ±D (in bar). [Value: [P:D]] [-pt] (■)
-nsm = Number of solvent molecules in the clustering process. [Value: I] [-ns](●)(■)
-bmc = Molal conc. of the microsolvation cluster (in mol·kg⁻¹). [Value: I] [-bc](●)(■)
-grp : Extract short-ranged non-bonded potential energies. [-gr] (■)
-nbx : Don´t make corrections for “fragmented” molecules near the box edges. [-nb] (■)
+ ----------------------------------------------------------
-prs = Include pressure configuration for thermodinamic calculation. [Value: N] [-pr]
-tmp = Include temperature configuration for thermodinamic calculation. [Value: N] [-tp]
-fcc = Final concentration after compression (in mol·L⁻¹). [Value: N] [-cf]
-frq = Scale factor for frequencies (for zero-point energy correction). [Value: N] [-sf]
-qha = Quasi-Harmonic Approximation (with optional cutoff frequency). [Value: <N>] [-fq]
-------------------------------------------------------------------------------------------------
(*) I,J = Integers; N,P,D = Real. (○) xTB available. (●) ORCA available. (■) GROMACS available.
4.1.2. FILES#
Input/output file Management
--------------------------------------------------------- files ⟨solute+solvent_molN.ext⟩ [⟨-options⟩] PARAMETERS input.ext [Output LOG/OUT/XTB file] OPTIONS -cpt [Compact the intermediate files] [Default: No] [-cp] -ext [Extract the intermediate files] [Default: No] [-ex] ---------------------------------------------------------
4.1.3. SOLVS#
List of available solvents and ions for packaging
---------------------------------------------------- solvs [<solvent>] [<-option>] OPTIONS/DEFAULTS -field T [Force field parameters] ► ALL = All force fields ● OPL = OPLS-AA/L all-atom force field ○ LPG = OPLS-AA/L (from LigParGen) ○ QFC = OPLS-AA/L (from Q-Force) ● GRO = GROMOS96 54a7 force field ○ ATB = GROMOS96 54a7 (from ATB) ● CHM = CHARMM36 all-atom force field ● AMB = AMBER-GS force field ----------------------------------------------------
4.1.4. MDPAR#
List of available configuration files for MD simulations
--------------------------------------------------- mdpar [⟨-step N⟩] OPTIONS/DEFAULTS -step N [Step for extracting MDP parameters] ► 0/ALL = List all MDP files ○ 1/OPT = Box Optimization ○ 2/MIN = Energy Minimization ● 3/NVT = NVT Equilibration ● 4/NPT = NPT Equilibration ● 5/PRD = NPT Production ---------------------------------------------------
4.2. Biomolecular Treatment#
4.2.1. PDBIO#
PDB processor for Biomolecular systems
------------------------------------------------------------- pdbio ⟨input.pdb⟩ [⟨-options⟩] PARAMETERS input.pdb [Input PDB file] output.gro/itp [Output GRO/ITP file] OPTIONS/DEFAULTS -ffp T [Force field parameters] [Default: OPLS] * GRO = GROMOS96 54a7 force field * OPL = OPLS-AA/L all-atom force field ADDITIONAL -pdb [Archives PDB input] -gro [Generate GRO geometry file] -itp [Produces ITP forcefield file] -ion [Don't do ITP files of ionic species] -lap [Override PDB input file] -cls [Wipe all PDB comment lines] -bak [Create a backup of auxiliary files] -------------------------------------------------------------
4.2.2. PDB2X#
PDB cleaner module
-------------------------------- pdb2x ⟨input.pdb⟩ [⟨-options⟩] PARAMETERS input.pdb [Input PDB file] output.ent [Output ENT file] --------------------------------
4.2.3. IONIC#
PDB ions forcefield constructor
------------------------------------ ionic ⟨input.pdb⟩ [⟨-options⟩] PARAMETERS input.pdb [Input PDB file] output.gro/itp [Output GRO/ITP file] ------------------------------------
4.2.4. GROUT#
GRO files processor module
------------------------------------------------------------- grout ⟨input.gro/itp⟩ [⟨-options⟩] PARAMETERS input.gro/itp [Input GRO/ITP file] output.gro/itp [Output GRO/ITP file] OPTIONS -gro [Archives GRO input/output] -itp [Produces a concatenated ITP forcefield file] -pdb [Converts a PDB file to GRO input geometry] -------------------------------------------------------------
4.2.5. GRO2X#
GRO cleaner module
------------------------------------ gro2x ⟨input.gro/itp⟩ [⟨-options⟩] PARAMETERS input.gro/itp [Input GRO/ITP file] output.gro/itp [Output GRO/ITP file] ------------------------------------
4.2.6. GROTC#
GRO total charge calculator
------------------------------- grotc ⟨input.gro⟩ PARAMETERS input.gro [Input GRO file] -------------------------------
4.3. Microsolvation Treatment#
4.3.1. CONFS#
Conformational analysis automator
------------------------------------------------------------------- confs ⟨input.ext⟩ [⟨-options⟩] PARAMETERS input.ext [Input COM/LOG/INP/OUT/XYZ/XTB/GRO/PDB file] OPTIONS -xff [Use GFN-FF in conformational analysis (default)] [-xf] -xtb [Use GFN2-xTB in conformational analysis (slower)] [-xt] -key T [Keywords for final optimization («xTB Opt Freq»)] [-kw] -svt T [Include implicity solvation configuration] [-sv] -prs N [Pressure for thermochemistry calculation (in atm)] [-ps] -tmp N [Temperature for thermochemistry calculation (in K)] [-tp] -con N [Final concentration after compression (in mol·L⁻¹)] [-fc] -min N [minimum Boltzmann weight for free energy averaging] [-mp] -prc P [Number of processors to be used] [-pc] -mem M [Amount of memory to use in GB] [-mm] -deb [Check generated inp file before submit] [-db] -for [Execute in forced mode] [-fm] OUTPUT FORMATS -inp [Output file in ORCA format (default)] [-in] -gro [Output file in GROMACS format] [-gr] -pdb [Output file in PDB format (for LigParGen)] [-pd] -xyz [Output file in XYZ format (for LigParGen)] [-xy] -sep [Split the output file into its conformers] [-sp] ------------------------------------------------------------------- NOTE: This is an interface to CREST program.
4.3.2. BONDS#
Hydrogen bonds analyzer
------------------------------------------------------------------- bonds ⟨input.ext⟩ [⟨-options⟩] PARAMETERS input.ext [Input COM/LOG/INP/OUT/XYZ/XTB/GRO/PDB file] OPTIONS -xff [Use GFN-FF in conformational analysis (default)] [-xf] -xtb [Use GFN2-xTB in conformational analysis (slower)] [-xt] -key T [Keywords for final optimization («xTB Opt Freq»)] [-kw] -svt T [Include explicit solvent and PCM configuration] [-sv] -prs N [Pressure for thermochemistry calculation (in atm)] [-ps] -tmp N [Temperature for thermochemistry calculation (in K)] [-tp] -con N [Final concentration after compression (in mol·L⁻¹)] [-fc] -min N [minimum Boltzmann weight for free energy averaging] [-mp] -prc P [Number of processors to be used] [-pc] -mem M [Amount of memory to use in GB] [-mm] -deb [Check generated inp file before submit] [-db] -for [Execute in forced mode] [-fm] PROCEDURES -nci N [Use CREST/NCI procedure with N svt mol] [-nc] -hbd N [Use CREST/HBD procedure with N svt mol] (default) [-hb] ------------------------------------------------------------------- NOTE: This is an interface to CREST and ORCA programs.
4.3.3. GSOLV#
Solvation Gibbs Free Energy Calculator
Under development...
4.3.4. MSRUN#
Microssolvation Aggregator
---------------------------------------------------------------------------------------------------- msrun ⟨simbox.trj.xyz⟩ [⟨-options⟩]⁽ᵃ⁾ msrun ⟨solute.trj.xyz⟩ [⟨-options⟩]⁽ᵇ⁾ PARAMETERS ⟨simbox.ext⟩ [Input simbox TRJ.XYZ file] ⟨solute.ext⟩ [Input solute TRJ.XYZ file] PROCEDURES -auto [Execute an automated microsolvation optimization] [-ac] -gcc C [GCALC module configuration. ( Ex.: -gc "-ini -opt -max 100 -fca" )] [-gc]⁽*⁾ -que C [QUEUE module configuration. ( Ex.: -qc "-key “#ONIOM(M062X/6-311+G(d,p):xTB)...”" )] [-qc]⁽*⁾⁽†⁾ OPTIONS -prc N [Number of parallel CPU processes to run] [Default: 8] [-pc] -mem N [Amount of memmory to be used (in GB)] [Default: 16] [-mm] ---------------------------------------------------------------------------------------------------- ⁽ᵃ⁾ From extracted tractory file (with TRAJS). [Complete procedure by default] ⁽ᵇ⁾ From extracted clusters file (with MICRO). [Partial procedure, without MICRO reexecution] ⁽*⁾ Each module can be run independently. ⁽†⁾ The “-key” option can be passed separately.
4.3.5. GCALC#
Gibbs Free Energy Calculator
-------------------------------------------------------------------------------------------------- gcalc ⟨solute.trj.xyz⟩ [⟨-options⟩] PARAMETERS ⟨solute.ext⟩ [Input solute TRJ.XYZ file] PROCEDURES -auto [Execute an automated microsolvation optimization] [-ga] » NOTE: this option is recommended in queue systems. » HINT: -auto [starts processing 100 clusters] : -auto N [starts processing N clusters] : -auto +M [add M clusters to the previous analysis] STEPS CONTROL ● Stage #1: Clusters Characterization [-s1]⁽▪⁾ -ini [Execute clusters characterization and selection] [Default: Auto] [-ic] Characterization for structures selection. Procedure performed at xTB-GFF level. ● Stage #2: Clusters Treatment [-s2]⁽▪⁾ -opt [Optimization and free energy calculation] (FSA|FCA|FCO) [Default: FCA] [-op] Calculation after structures selection Procedure performed at xTB-GFN2 level combined with DFT » FSA: [F]ull [S]olutes [A]ccommodated geometry (with SPH).¹ «xTB level» » FCA: [F]ull [C]luster [A]ccommodated geometry (with SPH).¹ «xTB level» » FCO: [F]ull [C]luster [O]ptimized geometry (with CHM).² «xTB level» ADITIONAL OPTIONS ● Selection Options -max M [Maximum number of structures into energy window] [Default: 100] [-nw]⁽*⁾ -add M [Add M clusters to GFE procedure from INI step. [Default: Not defined] [-ad]⁽*⁾ ● System Options -chr N [Value of microsolvated solute charge] [Default: Auto] [-ch]⁽*⁾ -mlt N [Value of microsolvated solute multiplicity] [Default: Auto] [-ml]⁽*⁾ -prs P [Pressure for thermochemistry calculation (in atm)] [Default: Auto] [-ps]⁽*⁾ -tmp T [Temperature for thermochemistry calculation (in K)] [Default: Auto] [-tp]⁽*⁾ ● Solvation Options -svt S [Solvent type (for ALPB/CPCM solvation method)] [Default: Auto] [-sv]⁽*⁾ -nis [No implicit solvation] [Default: None] [-ni]⁽*⁾ ● Configuration Options -prc N [Number of parallel CPU processes to run] [Default: 8] [-pc]⁽*⁾ -mem M [Amount of memmory to be used (in GB)] [Default: 16] [-mm]⁽*⁾ ● Additional Options -key T [“List of keywords” (for ONIOM program)] [Default: None] [-kw]⁽*⁾ -fcc N [Final concentration after compression] [Default: 1.0 mol·kg⁻¹] [-fc]⁽*⁾ -hbd [Include H-bonds at extrapolation (for ORCA final step). [Default: No] [-nm]⁽*⁾ -nmr [Config. for NMR calculation (for ORCA final step). [Default: No] [-nm]⁽*⁾ -for [Force reexecution stages. [Default: No] [-fm]⁽*⁾ -fil [Filter high energy clusters (above 100.0 kcal·mol⁻¹). [Default: No] [-fi]⁽*⁾ + ---------------------------------------------------------- -dat [Extract data for selected stage. [Default: No] [-dt]⁽*⁾ -plt [Plot extracted data. [Default: No] [-pd]⁽*⁾ -bak [Save generated graphs (without iterative interface). [Default: No] [-bk] + ---------------------------------------------------------- -exc [i,..][List of structural clusters to exclude. (inp) [i,j,k,...] [Default: None] [-ex]⁽†⁾ -clr [i,..][List of optimized clusters to clean. (out) [i,j,k,...] [Default: None] [-cl]⁽‡⁾ + ---------------------------------------------------------- -del N [Delete specified previous optimization] [Default: No] [-dc] -ext N [Extract specified previous calculation] [Default: No] [-ec] -ren T [Rename specified previous description] “DSC” / [OLD:NEW] [Default: No] [-rn] -chk [Check all previous calculations] (= spec. to extract) [Default: No] [-ck] -log [Summary of performed calculations] [Default: No] [-lg] + ---------------------------------------------------------- -out T [Force reading specified ONIOM output file] [Default: No] [-of] [Force reading default ONIOM output file] [Default: No] [-of] + ---------------------------------------------------------- -bnd [Execute in BONDS mode] [Default: No] [-bd] -------------------------------------------------------------------------------------------------- ⁽*⁾ Configurable options in automated mode. ⁽▪⁾ Try “-sN” to view stage N only. ⁽†⁾ The “ith” cluster identified from trj.xyz input file. ⁽‡⁾ The “ith” cluster identified through graphical analysis. ⁽¹⁾ SPH = Single Point Hessian. ⁽²⁾ CHM = Conventional Hessiam Method.
4.3.6. QUEUE#
QUEUE System Manager
-------------------------------------------------------------------------------------------------- queue [⟨-options⟩] OPTIONS -inf [Show current ONIOM calculation configuration] [-if] -log [Show current ONIOM calculation results] [-lg] -run [Perform the calculation procedure] [-rc] + ---------------------------------------------------------- -key T [Complete list of keywords for ONIOM calculation configuration] [-kw] -chr N [Charge value of the microsolvation cluster] [-ch] -mlt N [Multiplicity value of the microsolvation cluster] [-ml] -des T [Optional output configuration description] [-ds] -fcc N [Final concentration after compression] [Default: 1.0 mol·kg⁻¹] [-fc] -con [Force concatenation of results over warnings] [-cd] -clr [Clean up run folder after archiving results] [-cr] + ---------------------------------------------------------- -srm [Execute calculation in a serial mode] [-sr] -for [Execute calculation in forced mode] [-fm] + ---------------------------------------------------------- -bnd [Execution for BONDS module] [Default: No] [-bd] -gcc [Execution for GCALC module] [Default: Yes] [-gc] + ---------------------------------------------------------- -prc N [Number of parallel CPU processes to run] [Default: 8] [-pc] -mem N [Amount of memmory to be used (in GB)] [Default: 16] [-mm] --------------------------------------------------------------------------------------------------
4.3.7. ONIOM#
ONIOM Program
---------------------------------------------------------------------------------------- oniom ⟨input.gjf⟩ [⟨-options⟩] PARAMETERS ⟨input.gjf⟩ [File with GaussView format for Solvate/Microssolvation calculation] OPTIONS -opt [Execute geometry optimization in forced mode] [Default: No] [-op] -ext [Execute ONIOM extrapolation in forced mode] [Default: No] [-ex] + ---------------------------------------------------------- -srm [Execute calculation in a serial mode] [Default: No] [-sr] -for [Execute optimization and extrapolation in forced mode] [Default: No] [-fm] -deb [No extrapolation execution: only tests] [Default: No] [-ne] + ---------------------------------------------------------- -prc N [Number of parallel CPU processes to run] [Default: 8] [-pc] -mem N [Amount of memmory to be used (in GB)] [Default: 16] [-mm] ----------------------------------------------------------------------------------------
4.4. Multiple Purposes#
4.4.1. CHECK#
Monitoring of procedures progress
-------------------------------------------------------------------- check ⟨input.ext⟩ [⟨compt.ext⟩] [⟨-options⟩] PARAMETERS input.ext [Input file] compt.ext [Compacted file] [Extensions: COM/INP/XYZ/LOG/OUT/XTB/TMP] OPTIONS -ext [Extract compacted internal file] (ex.: check inpfile.zip cptfile.cpt -ext) -del [Deletes compacted internal file][zip only] (ex.: check inpfile.zip cptfile.cpt -del) -ren [Renames compacted internal file][zip only] (ex.: check inpfile.zip oldfile.cpt -ren newfile.cpt) --------------------------------------------------------------------
4.4.2. CLEAN#
Cleaner for temporary files
4.4.3. COMPT#
Compression of output files
---------------------------------------- compt ⟨output.log/out/xtb⟩ [-chk] PARAMETERS output.ext [Output LOG/OUT/XTB file] ----------------------------------------
4.4.4. DEPLY#
Full deployment Python dependencies check
4.4.5. IMAGS#
Imaginary mode distortion
---------------------------------------- imags <output.log/out/xtb> [-img fator] PARAMETERS output.ext [Output LOG/OUT/XTB file] ----------------------------------------
4.4.6. INFOS#
Displaying system information
4.4.7. MOLAP#
Structural alignment for RMSD minimization
------------------------------------------------------------------------------------------- molap ⟨reference.ext⟩ ⟨structure.ext⟩ [⟨trajectory.trj.xyz⟩] [⟨-options⟩] PARAMETERS files.ext [Input COM/LOG/INP/OUT/XYZ/XTB/GRO/PDB file] OPTIONS -bak [Save modified “structure” file with minimized RMSD (at system origin)] [-bk] -ref [Save modified “structure” file with minimized RMSD (at “reference” center)] [-rf] -str [Save modified “structure” file with minimized RMSD (at “structure” center)] [-st] -slt [Reorientation relative to the central solute fragment] [-sf] -------------------------------------------------------------------------------------------
4.4.8. RMSDS#
Calculation of structural RMSD and solute energy
------------------------------------------------------------------------------------ rmsds ⟨reference.ext⟩ ⟨structure.ext⟩ [⟨preoptimization.ext⟩] [⟨trajectory.trj.xyz⟩] PARAMETERS input.ext [Output COM/LOG/INP/OUT/XYZ/XTB/GRO/PDB file] OPTIONS -min [Maximum structural superposition for RMSD minimization] [-mr] -bak [Save RMSD information in the input “structure” file] [-bk] -for [Force new calculation and override previous output] [-fm] ------------------------------------------------------------------------------------
4.4.9. SCALC#
Chemical shifts calculator
--------------------------------------------------------------------------- scalc ⟨input.trj.xyz⟩ [⟨-options⟩] PARAMETERS input.trj.xyz [Output TRJ file] OPTIONS -ato A [Atomic symbol of the species to be analyzed] [-at] -ref N [Reference value for chemical shifts (in ppm)] [-rf] -eqv [L] [List of equivalent atoms. (note: -eqv=[A1=A2:B1=B2=B3...])] [-eq] +----------------------------------------------------------+ -out F [Force reading specified ONIOM output file] [-of] -out [Force reading default ONIOM output file] [-of] +----------------------------------------------------------+ -hbd [Use BONDS data] [-hb] -gcc [Use GCALC data] [-gc] -plt [Plot the NMR spectrum] [-pt] --------------------------------------------------------------------------- * Note : Requires “gcc” file, and optionally “pcm” and “exp” files.
4.4.10. SOLVX#
Solvent identifier in clusters
------------------------------------ solvx ⟨file.trj.xyz⟩ PARAMETERS file.trj.xyz [Output TJR.XYZ file] ------------------------------------
4.4.11. STAND#
Modify input to standard orientation
------------------------------------------ stand ⟨input.ext⟩ & PARAMETERS input.ext [Input GJF/COM/INP/XYZ/GRO] ------------------------------------------
4.4.12. STATX#
Full statistical analysis directly from GMX program
--------------------------------- statx ⟨output.log⟩ PARAMETERS output.log [Output LOG file] ---------------------------------
4.4.13. SUBST#
Modification of texts in editable files
--------------------------------- subst ⟨input.ext⟩ "text1" "text2" PARAMETERS input.ext [Extensions: all] ---------------------------------
4.4.14. SUMMY#
Extraction of properties from output files
--------------------------------------------------------------------------------- summy ⟨output.log/out/xtb⟩ PARAMETERS output.ext [Output LOG/OUT/XTB file] OPTIONS/DEFAULTS -prs N [Pressure configuration for thermodinamic calculation] -tmp N [Temperature configuration for thermodinamic calculation] -fcc N [Final concentration after compression (in mol·L⁻¹)] -frq N [Scale factor for frequencies (for zero-point energy correction)] -qha <N> [Quasi-Harmonic Approximation (with optional cutoff frequency)] ---------------------------------------------------------------------------------
4.4.15. SUPPY#
Extraction of supplementary data from output files
--------------------------------------------------------------------------------- suppy ⟨output.log/out/xtb⟩ PARAMETERS output.ext [Output LOG/OUT/XTB file] OPTIONS/DEFAULTS -prs N [Pressure configuration for thermodinamic calculation] -tmp N [Temperature configuration for thermodinamic calculation] -fcc N [Final concentration after compression (in mol·L⁻¹)] -frq N [Scale factor for frequencies (for zero-point energy correction)] -qha <N> [Quasi-Harmonic Approximation (with optional cutoff frequency)] ---------------------------------------------------------------------------------
4.4.16. SVIEW#
Visualization of input/output files
-------------------------------------------------------------------------------- sview ⟨input.ext⟩ [⟨-options⟩] & PARAMETERS input.ext [Input file]⁽*⁾ GENERAL OPTIONS -try I [Generate a try file with N truncated steps (.trj file)] -vmd [Force file open with VMD program] -cpt [Perform compression of input/output files for GVW program] JMOL OPTIONS -noc [Run without input convertion] VMD OPTIONS -cpk [Show solute with VDW representation] -vdw [Show solute with VDW representation] -lico [Activate Licorice for solvent shell] -dyna [Activate DynamicBonds for solvent shell] -surf [Activate QuickSurf for solvent shell] -text [Execute in a text mode] -------------------------------------------------------------------------------- ⁽*⁾ Conversions: COM/GJF/LOG/INP/OUT/XYZ/XTB/PDB/GRO/TRJ
4.5. Queuing Systems#
4.5.1. SUBMIT#
Run the program in the system queue
--------------------------------------------------- submit ⟨program⟩ ⟨input.ext⟩ ⟨-options⟩ ⟨-ntasks I⟩ PARAMETERS program [gsn/orca/xtb/gmx program] input.ext [Input GJF/COM/INP/XYZ/GRO file] OPTIONS/DEFAULTS -options [Program specific options] -queue T [Name of available queue] -ntasks I [Number of processors] [-prc] -qmemor I [Amount of memory (in GB)][-mem] -preserve [Preserve the submission job file] -debug [Check generated job before submit] AVAILABLE SYSTEM BATCH »Local Machine WARNING This is an open-source script that may require adjustments depending on the available queue system ---------------------------------------------------
4.6. Program Interfaces#
4.6.1. runORCA#
ORCA program interface [Program Manual]
4.6.2. runCP2K#
CP2K program interface [Program Manual]
4.6.3. runXTB#
xTB program interface [Program Manual]
4.6.4. runCREST#
CREST program interface [Program Manual]
4.6.5. runMOPAC#
MOPAC program interface [Program Manual]
4.6.6. runGROMACS#
GROMACS program interface [Program Manual]
4.6.7. runBABEL#
oBabel program interface [Program Manual]
4.6.8. runJMOL#
JMol program interface [Program Manual]
4.6.9. runVMD#
VMD program interface [Program Manual]
4.6.10. runPACKMOL#
PackMol program interface [Program Manual]
4.6.11. runQFORCE#
Q-Force program interface [Program Manual]