3.2. Usual Parameters

In this page is presented the mandatory parameters for all run, along with the most common ones.

3.2.1. To deal with the MD trajectory

GlobalParameter.MD_file_name_topology

Type [string]

The name of the molecular dynamic topology file, used to defined which atom are part of the same molecules. Apart from that, the molecule names, groups, masses or other informations is not taken into account. FROG is not designed to handle changes in the topology files in time. More informations about the supported topology files are available here. Even if the file is located in the working directory, we strongly recommend to use general path:

GP.MD_file_name_topology = '/home/user/MD/mytopology.data'

Warning

Mandatory parameter

GlobalParameter.MD_file_name_traj

Type [string]

The name of the molecular dynamic trajectory file. This file should respect the topology defined in GlobalParameter.MD_file_name_topology . More informations about the supported trajectory files are available here. Even if the file is located in the working directory, we strongly recommend to use general path:

GP.MD_file_name_traj = '/home/user/MD/mytrajectory.dcd'

Warning

Mandatory parameter

GlobalParameter.MD_file_type

Type [string]

The type of topology and trajectory used as input, in GlobalParameter.MD_file_name_topology and GlobalParameter.MD_file_name_traj respectively. The type used have to be compatible with the MDAnalysis. python module. More informations about the supported MD output are available here.

Example

For an LAMMPS output, use:

GP.MD_file_name_topology = '/home/user/MD/mytopology.data'
GP.MD_file_name_traj = '/home/user/MD/mytrajectory.dcd'
GP.MD_file_type = 'LAMMPS'

You can try to open your topology/trajectory if you have trouble to deal with these parameters in Frog. To open the MD trajectory with MDAnalysis, Frog use:

u = MDAnalysis.Universe(GP.MD_file_name_topology, GP.MD_file_name_traj, format=GP.MD_file_type)

Note

Do not hesitate to try out combinaison of topology-trajectory which would have not been yet presented in the doc and to send us feedback for any working combinaison.

Warning

Mandatory parameter

GlobalParameter.MD_convertion_to_angstrom

Type [float]

The convertion to apply to get the distance of the MD trajectory in Angstrom. If not provieded, Frog assume that the unit of the MD is already Angstrom.

Example

If you want to rescale your MD trajectory by 0.529177, use:

GP.MD_convertion_to_angstrom = 0.529177

Position used by frog = (Position MD) x (GP.MD_convertion_to_angstrom)

Note

Use float not integer – 1.0 instead of 1 for instance.

Note

There is no real need to use Angstrom unit. You just have to be coherent with the values defined everywhere in Frog and in the Molecular library file. Be aware that the Anstrom unit are expected in the current procedure with Dalton.

GlobalParameter.MD_cut_trajectory

Type [boolean]

If set to True, the trajectory will be cut in several file in order to have one time step per file. This option is made in order to reduce the RAM memory needed. The piece of trajectory are saved in the GP.dir_mol_times directory. By default True.

Example

GP.MD_cut_trajectory = True

Note

If you deal with a very small trajectory, it may not worth it to cut it: set GP.MD_cut_trajectory. Otherwise, it seems a good safe-guard to avoid impacting the initial trajectory. Indeed, the initial trajectory will be read at the very begining of the Frog run to perform the cut, and then will not be open again.

GlobalParameter.nbr_time_step

Type [integer]

Define the total number of frame to treat. If set to 0, treat the maximal frame number possible depending on the total number of frame available in the MD trajectory and the value of GlobalParameter.trotter_step . The default value is 1.

Example

GP.nbr_time_step = 80
GP.trotter_step = 4

Will treat the MD snapshot each 4 available frame up to 80, ie the frame number 1, 5, 9, …

GP.nbr_time_step = 0
GP.trotter_step = 10

If the MD trajectory contains 100 frames, FROG will treat 10 snapshot separated by 10 frames, ie the frame 1, 11, .. 101

GlobalParameter.trotter_step

Type [integer]

How many consecutive frame are not treated (1 means every frame are treated, 2, only one over 2, ect..). The default is 1. See GlobalParameter.nbr_time_step for more information.

GlobalParameter.env_authorised_pbc_condition

Type [list]

Defines which direction can be used to built environment is needed. By default all 3 direction are supposed to be PBC.

Example

GP.env_authorised_pbc_condition = [0, 1]

In this case, only the X and Y direction are understood as PBC.

Warning

FROG has been tested for 3D and 2D PBC. If you are using no PBC condition, you may want to be carefull…

GlobalParameter.layer_which_radii_MT

Type [str or dict]

Defines how to set the VDW radii used by pytim to attributes layer to the molecule. Precisely, the radii is the optional argument ‘radii_dict’ of the function pytim.ITIM, see https://marcello-sega.github.io/pytim/guessing_radii.html

Possible values:

• ‘MD’: No values are set manually. Therefore, pytim try to use the Gromos 43A1 force field to attribute radii.

• ‘MT’: default value, uses the values defines in the MT, using the function info_molecule_for_layer of the molecular library file. Note that if this option is used, the GP.MD_cut_trajectory is set to True. Indeed, Frog needs to modify the topology file in order to make this option work.

• your_dict: you can pass directly a dictionary, which will be used as pytim.ITIM(u, radii_dict = your_dict). The name of the directory does not matter: it just has to be a directory so that this option is detected by Frog.

3.2.2. Functionement parameters

GlobalParameter.nbr_parra

Type [integer]

Maximal number of core on which the first and third part of the run will be parralelized. This is number is NOT related to the parralelization of the QM runs. OpenMP is required to performed this parralelization. The default value is 1.

Example

GP.nbr_time_step = 80
GP.nbr_parra = 2

The total number of frame treat is 80, and 2 cores will be used. Each core will treat 40 frames.

GP.nbr_time_step = 5
GP.nbr_parra = 2

The total number of frame treat is 5, and 2 cores will be used. One core will treat 3 frames, the other 2.

Note

If GP.nbr_parra > GP.nbr_time_step, the GP.nbr_parra is set to GP.nbr_time_step.

Note

Be aware that the RAM may become important, so do not overload your (personal) computer and try small GP.nbr_parra to start with.

Note

If you use parallelization, it is recommanded to cut the MD trajectory to not overload the RAM and for savety (of the MD trajectory file: otherwise it would be read by several core at the same time.). Set GP.MD_cut_trajectory to True (default value).

GlobalParameter.pass_first_part

Type [bool]

Defined if the first part should be perform or not. This appribute has been created to deal with QM calculation.

Default value False: Frog perform the first part and overwrite the previous results.

If set to True, the first part of the run will be skiped if possible all the moleculetype file are found in the dir_mol_times directory for every time step required.

Note

Frog do not check if the input file is the same for the previous calculation used for the restart, and the one provided (which have launch this calculation). The MT object are the same as the one defined in the previous calculation, while the GP is the one of the new parameters. This has been done in order to make possible to change the attribute relative to the QM management – in the GP parameters.