How to execute CONFLEX

[Input files]

In CONFLEX, a structure file that describes structure data of a molecule/crystal and an ini file that describes keywords for calculation settings are used as input files. You can use the structure file of MOL/MOL2/PDB/CIF/CMF format. Name of the structure and ini files has to match excepting for suffix. The suffix of the ini file is “.ini”. These input files have to be stored in an one folder when executing CONFLEX.
If you execute CONFLEX by CONFLEX Interface, the ini file is automatically created by CONFLEX Interface.
On the other hand, in case of executing CONFLEX from a command line, you need to make the ini file in advance. You can also execute CONFLEX without the ini file. In that case, calculations of molecular structure optimization and normal mode analysis are performed in default setting.

Execution by CONFLEX Interface (Windows/Mac/Linux)

Launch CONFLEX Interface.

Either select [Open] in File menu and specify the structure file or drug & drop the structure file to the gray part of CONFLEX Interface. A molecule will be displayed.

Next, select [CONFLEX] in Calculation menu. A calculation setting dialog will be displayed.

Click Submit. Calculations of molecular structure optimization and normal mode analysis will be performed in default setting.

If you want to perform other calculations, either select an other option in the pull-down menu of [Calculation Type:] or click Detail Settings and open a detail setting dialog.

In [General Settings] dialog on the detail setting dialog, you can select another calculation from the pull-down menu of [Calculation Type:].
In the detail setting dialog, you can make various calculation settings in detail. Please refer to detail setting manual of CONFLEX Interface for using the detail setting dialog.

When you complete the settings, click Submit. The calculation will start.

On the other hand, if you click Edit & Submit, a dialog will open.

In CONFLEX, the calculation settings are defined by describing keywords in the (structure filename).ini file.
The descriptions in the above dialog are the keywords and CONFLEX Interface automatically makes the (structure filename).ini that describes the keywords in the dialog.
You can edit the keywords in the dialog and add new keywords to the dialog.
When you complete the adding and editing, click Submit. The calculation will start.

[How to use Parallel CONFLEX]

In the detail setting dialog, you can make settings of parallel calculation.

• [Parallel search per Node#:] defines the number of processes in a search calculation parallelized by MPI.
• [Parallel Optimize #:] defines the number of threads in a process of optimization calculation parallelized by OpenMP.

In a conformation search and crystal structure search, you can use the two parallelization above at the same time. In this case, the job spends the number of CPU cores equals to values obtained by multiplying the value of [Parallel search per Node#:] by the value of [Parallel Optimize #:].

[Execution by command line (Windows)]

Prepare the structure file and the ini file as inputs. You can use the structure file of MOL/MOL2/PDB/CIF/CMF format. Name of the structure and ini files has to match excepting for suffix. Here, we use Cyclohexane.mol and Cyclohexane.ini files in [C:\CONFLEX\Sample_Files\CONFLEX\optimization_and_search].
Create a “Test” folder on Desktop, and copy both the files to the Test folder.

The Cyclohexane.ini file describes keywords of calculation settings. About an explanation of the keywords, please refer to a manual.

Next, launch a command prompt

Execute below command. The current directory will change to the Test folder.

cd   C:\Users\conflex\Desktop\Test
enter

* The “conflex” in above address is account name. For example, when your account name is “guest”, the above address is “C:\Users\guest\Desktop\Test.”

Next, execute below command. The files in the Test folder will be listed.

dir
enter

There are two files, Cyclohexane.mol and Cyclohexane.ini.

Execute below command. A calculation will start.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   Cyclohexane
enter

* The option of “-par” in the command specifies an address of folder containing parameter files. The last argument in the command is the name of structure file excepting the suffix.

[How to use Parallel CONFLEX]

The number of threads in a process of optimization calculation sets by an option of “-omp” in the execution. The number of processes in a search calculation sets by an option of “-np” in “mpiexec.exe” program.

If you want to parallelize a optimization calculation parallelized, execute CONFLEX by below command.

C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par   -omp   [the number of threads]   [structure file name(no suffix)]
enter

If you want to parallelize a search calculation parallelized, execute CONFLEX by below command. It is note that the CONFLEX filename in the below command is different from the above command.

C:\CONFLEX\bin\mpiexec.exe   -np   [the number of processes]   C:\CONFLEX\bin\flex9a_MPI_win_x64.exe   -par   C:\CONFLEX\par   [structure file name(no suffix)]
enter

When you want to parallelize both the search and optimization calculations, execute CONFLEX by below command.

C:\CONFLEX\bin\mpiexec.exe   -np   [the number of processes]   C:\CONFLEX\bin\flex9a_MPI_win_x64.exe   -par   C:\CONFLEX\par   -omp   [the number of threads]    [structure file name(no suffix)]
enter

Each parallelization of optimization and search is implemented by OpenMP and MPI, respectively. The options of “-omp” and “-np” are for setting the number of parallels in OpenMP and MPI, respectively.

[Execution by command line (Linux)]

Prepare the structure file and the ini file as inputs. You can use the structure file of MOL/MOL2/PDB/CIF/CMF format. Name of the structure and ini files has to match excepting for suffix. Here, we use Cyclohexane.mol and Cyclohexane.ini files in [/usr/local/conflex/Sample_Files/CONFLEX/optimization_and_search/].

First, launch a terminal.

Execute below commands, create a “Test” folder in Home directory, and copy both the files to the Test folder.

mkdir   ~/Test
enter
cp   /usr/local/conflex/Sample_Files/CONFLEX/optimization_and_search/Cyclohexane.mol   ~/Test
enter
cp   /usr/local/conflex/Sample_Files/CONFLEX/optimization_and_search/Cyclohexane.ini   ~/Test
enter

Execute below command. The current directory will change to the Test folder.

cd   ~/Test
enter

Next, execute below command. The files in the Test folder will be listed.

ls  　-l
enter

There are two files, Cyclohexane.mol and Cyclohexane.ini.
The Cyclohexane.ini file describes keywords of calculation settings. About an explanation of the keywords, please refer to a manual.

Execute below command. A calculation will start.

/usr/local/conflex/flex9a.Linux.exe   -par   /usr/local/conflex/par   Cyclohexane
enter

* The option of “-par” in the command specifies an address of folder containing parameter files. The last argument in the command is the name of structure file excepting the suffix.

[How to use Parallel CONFLEX]

The number of threads in a process of optimization calculation sets by an option of “-omp” in the execution. The number of processes in a search calculation sets by an option of “-np” in “mpiexec.exe” program.

If you want to parallelize a optimization calculation parallelized, execute CONFLEX by below command.

/usr/local/conflex/flex9a.Linux.exe   -par   -omp   [the number of threads]   [structure file name(no suffix)]
enter

If you want to parallelize a search calculation parallelized, execute CONFLEX by below command. It is note that the CONFLEX filename in the below command is different from the above command.

/usr/local/conflex/bin/mpirun   -np   [the number of processes]   /usr/local/conflex/bin/flex9a.MPI.Linux.exe   -par   /usr/local/conflex/par   [structure file name(no suffix)]
enter

When you want to parallelize both the search and optimization calculations, execute CONFLEX by below command.

/usr/local/conflex/bin/mpirun   -np   [the number of processes]   /usr/local/conflex/bin/flex9a.MPI.Linux.exe   -par   /usr/local/conflex/par   -omp   [the number of threads]   [structure file name(no suffix)]
enter

Each parallelization of optimization and search is implemented by OpenMP and MPI, respectively. The options of “-omp” and “-np” are for setting the number of parallels in OpenMP and MPI, respectively.

[Execution by command line (Mac)]

Prepare the structure file and the ini file as inputs. You can use the structure file of MOL/MOL2/PDB/CIF/CMF format. Name of the structure and ini files has to match excepting for suffix. Here, we use Cyclohexane.mol and Cyclohexane.ini files in Sample_Files folder.

First, launch a terminal. The program is in [Application] -> [Utility] -> [Terminal.app].

Execute below commands, create a “Test” folder in Home directory, and copy both the files to the Test folder.

mkdir   ~/Test
enter
cp   /Applications/CONFLEX/Sample_Files/CONFLEX/optimization_and_search/Cyclohexane.mol   ~/Test
enter
cp   /Applications/CONFLEX/Sample_Files/CONFLEX/optimization_and_search/Cyclohexane.ini   ~/Test
enter

Execute below command. The current directory will change to the Test folder.

cd   ~/Test
enter

Next, execute below command. The files in the Test folder will be listed.

ls   -l
enter

There are two files, Cyclohexane.mol and Cyclohexane.ini.
The Cyclohexane.ini file describes keywords of calculation settings. About an explanation of the keywords, please refer to a manual.

Execute below command. A calculation will start.

/Applications/CONFLEX/bin/flex9a.Mac.exe   -par   /Applications/CONFLEX/par   Cyclohexane
enter

* The option of “-par” in the command specifies an address of folder containing parameter files. The last argument in the command is the name of structure file excepting the suffix.

[How to use Parallel CONFLEX]

The number of threads in a process of optimization calculation sets by an option of “-omp” in the execution. The number of processes in a search calculation sets by an option of “-np” in “mpiexec.exe” program.

If you want to parallelize a optimization calculation parallelized, execute CONFLEX by below command.

/Applications/CONFLEX/bin/flex9a.Mac.exe   -par   /Applications/CONFLEX/par   -omp   [the number of threads]   [structure file name(no suffix)]
enter

If you want to parallelize a search calculation parallelized, execute CONFLEX by below command. It is note that the CONFLEX filename in the below command is different from the above command.

/Applications/CONFLEX/bin/mpirun   -np   [the number of processes]   /Applications/CONFLEX/bin/flex9a.MPI.Mac.exe   -par   /Applications/CONFLEX/par   [structure file name(no suffix)]
enter

When you want to parallelize both the search and optimization calculations, execute CONFLEX by below command.

/Applications/CONFLEX/bin/mpirun   -np   [the number of processes]    /Applications/CONFLEX/bin/flex9a.MPI.Mac.exe   -par   /Applications/CONFLEX/par   -omp   [the number of threads]    [structure file name(no suffix)]
enter

Each parallelization of optimization and search is implemented by OpenMP and MPI, respectively. The options of “-omp” and “-np” are for setting the number of parallels in OpenMP and MPI, respectively.