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Quick Start Guide
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Quick Start Guide
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Installation:
In folder "src", please use,
$make sDMD
to build the main simulation executable "sDMD". If users also would like to perform a replica-exchange molecular dynamics (REMD) simulation, please use,
$make all
to build the all three executables "sDMD", "sREMD" and "sServer".
In folder "analysis", please use,
$make
to build the analysis executable "sAnalysis".
Execution:
To perform a regular DMD simulation, please use,
$./sDMD [args]
The supported arguments and their descriptions can be shown by,
$./sDMD -h
To perform a REMD simulation, please place the three executables "sDMD", "sREMD" and "sServer" in the same directory and use,
$./sREMD [args]
The supported arguments and their descriptions can be shown by,
$./sREMD -h
To perform an analysis, please use,
$./sAnalysis [args]
The supported arguments and their descriptions can be shown by,
$./sAnalysis -h
File List:
analysis (folder of the source files of the analysis executable)
|- *.c
|- *.h
source files for the executable "sAnalysis".
|- Makefile
Makefile to compile and build the executable.
demo (folder of the outputs and analyzed results of the two illustrative examples)
|- Folding (folder of an example of a folding simulation)
|- analysis (folder containing the analyzed results)
|- Energy.txt
energy related results.
|- HBInfo.txt
hydrogen bond related results.
|- HBNum.pdb
plot of alpha hydrogen bond number vs simulation time.
|- PE.pdb
plot of potential energy vs simulation time.
|- Plot*.txt
scripts for "gnuplot" to plot the results.
|- ref_*.gro
reference structures of the poly-alanine to perform RMSD calculations.
|- RG.pdb
plot of radius of gyration vs simulation time.
|- RG.txt
radius of gyration results.
|- RMSD.pdb
plot of RMSD with respect to the native structure of the poly-alanine vs simulation time.
|- RMSD.txt
RMSD related results.
|- output (folder containing the dumping data)
|- out_cnt*.txt
dumping data of connection information.
|- out_log*.txt
dumping data of simulation log.
|- out_trj*.txt
dumping data of trajectory.
|- savedData*.dat
break point data files for the extended simulations.
|- SysInfo.dat
information of the simulated system (for analysis).
|- timeEvaluation.dat
data file for the time-cost prediction of the next simulation.
|- ala10.gro
coordinate input file of a poly-alanine in its native structure.
|- fold.bash
bash script to perform the entire folding simulation.
|- parameter.txt
configuration file to perform the simulation.
|- REMD (folder of the example of REMD simulation)
|- analysis (folder containing the analyzed results)
|- CombinedPotMap.txt
combined data of the potential energy surface of all the replicas.
|- CvPotT.txt
average potential energy and heat capacity vs simualtion temperature.
|- Energy*.txt
energy related results of each replica.
|- FreeEnergy.txt
potential of mean force at different temperature vs reaction coordinate.
|- FT.pdb
plot of the heat capacity (reduced) of the poly-alanine vs simulation temperature.
|- HBInfo*.txt
hydrogen bond related results of each replica.
|- PESurface.pdb
plot of the combined potential energy surface with respect to the reaction coordinates.
|- Plot*.txt
scripts for "gnuplot" to plot the results.
|- PMFMap_T*.txt
potential of mean force surface with respect to the reaction coordinates of each temperature.
|- PotMap_T*.txt
potential energy surface with respect to the reaction coordinates of each temperature.
|- PotMap*.txt
potential energy surface with respect to the reaction coordinates of each replica.
|- Probability.txt
probability distributions of the reaction coordinate values at different temperature.
|- ref_*.gro
reference structures of the poly-alanine to perform RMSD calculations.
|- RMSD*.txt
RMSD related results of each replica.
|- output (folder containing the dumping data)
|- out_cnt*.txt
dumping data of connection information.
|- out_log*.txt
dumping data of simulation log.
|- out_REMD*.txt
dumping data of REMD simulation information.
|- out_trj*.txt
dumping data of trajectory.
|- savedData*.dat
break point data files for the extended simulations.
|- SysInfo*.dat
information of the simulated systems (for analysis).
|- timeEvaluation.dat
data file for the time-cost prediction of the next simulation.
|- ala10.gro
coordinate input file of the native poly-alanine.
|- parameter.txt
configuration file to perform the simulation.
|- REMD.bash
bash script to perform the REMD simulation.
|- REMDConfig.txt
configuration file to perform the REMD simulation.
input (folder of the model library and the configuration files)
|- Library_Ding
|- AA (folder of the amino acid model)
|- *.txt
model file of each amino acid.
|- HBPotentialTable.txt
potential table for hydrogen bonding calculation.
|- InteractionPotentialTable.txt
potential table for non-bonded and bonded interactions.
|- Wall.txt
parameters of wall/surface.
|- ala10.gro
coordinate input file of a poly-alanine in its native structure.
|- parameter.txt
configuration file to perform the simulation.
|- REMDConfig.txt
configuration file to perform the REMD simulation.
src (folder of the source files of the simulation executables)
|- *.c
|- *.h
source files for the executables "sDMD", "sREMD" and "sServer".
|- Makefile
Makefile to compile and build the executables.