Sampling Trajectory Files

The used GROMACS trajectory is sampled using the ChemFiles package. In order to avoid artefacts due to periodic boundary conditions, molecules are joined using the -pbc mol command in GROMACS which places the center of mass of the molecules into the box. Furthermore, PoreAna only analyses one molecule type per routine, that’s why the desired molecule type has to be extracted first

gmx_mpi trjconv -f traj.xtc -s topol.tpr -o traj_mol.xtc -pbc mol

The sampling routine uses the molecule structure defined by the PoreMS package

import porems as pms

mol = pms.Molecule(inp="data/benzene.gro")
mol

    Residue Name Type      x      y      z
0         0   C1    C  0.196  0.108  0.109
1         0   C2    C  0.300  0.048  0.181
2         0   C3    C  0.295  0.046  0.320
3         0   C4    C  0.188  0.104  0.387
4         0   C5    C  0.084  0.163  0.315
5         0   C6    C  0.088  0.165  0.176
6         0   H1    H  0.199  0.110  0.000
7         0   H2    H  0.384  0.004  0.128
8         0   H3    H  0.376  0.000  0.376
9         0   H4    H  0.184  0.102  0.496
10        0   H5    H  0.000  0.208  0.368
11        0   H6    H  0.008  0.211  0.120

Before running the sampling routine, first a Sample object has to be created with the pore system (pore_syste.obj file provided by PoreMS), trajectory file, the corresponding molecule object and a list of atoms names to be considered (empty list for all)

import poreana as pa

sample = pa.Sample("data/pore_system_cylinder.obj", "data/traj_cylinder.xtc", mol, [])

The next step is activating the analysis routines to be used during the sampling process using the initialize functions with their corresponding inputs

sample.init_density("output/dens.h5")
sample.init_gyration("output/gyr.h5")
sample.init_diffusion_bin("output/diff.h5")

If you would like to calculated the diffusion and the free energy profile you have to set the MC Diffusion initalize function instead of the Bin Diffusion. Attention currently only the initialization of one diffusion calculation method is possible.

sample.init_density("output/dens.h5")
sample.init_gyration("output/gyr.h5")
sample.init_diffusion_mc("output/diff.h5")

Finally, the sample function is initiated with the option to run in parallel and deactivating the periodic boundary conditions

sample.sample(is_parallel=True, is_pbc=False)

Finished frame 2001/2001...