4. Samples

Author:Kota Kasahara

4.1. Sample files

Some sample simulation data are attached.

In following instruction, it is assumed that the variable $OMEGATK indicates the path to the omega_toolkit. And the binary omegagene is placed in a directory in ${PATH}, and the library files libCelesteCUDA.so and libCelesteCore.a are placed in ${LD_LIBRARY_PATH} directories.

4.1.1. NVE calculation (Trp-cage)

Move to the directory cal01_nve/run00001.

And execute the bash file:

bash 1_generate_velocities.bash

In this shell, the initial velocities are generated. See the output:

number of atoms: 13277
Number of rigid units: 4495
TEMPERATURE:300.0
[ 2.05517825e-11 4.44033144e-11 -9.32866839e-11]`

The last line indicates the momentum of COM in each axis.

Next, check the simulation setting in system.cfg and atom_groups.inp:

vi system.cfg
vi ../atom_groups.inp

Generate the input binary file:

bash 2_mdinput_gen.bash

The log is output in mdinpgen.out:

size: buf_pos_rest: 4
size: buf_group_coord: 0
End

Then, execute omegagene. Before that, check the setting file md.cfg:

vi md.cfg

Execute it:

bash 3_submit.bash

The directory run00002 is for test of restarting the calculation in run00001:

cd ../run00002
diff system.cfg ../run00001/
diff md.cfg ../run00001/
bash 4_mdinput_gen_2.bash
bash 5_submit_2.bash

Check the accordance of the energy values at the last of run00001 and the first of run00002.

4.1.2. Other ensembles

Some other samples can be performed in a similar way.

• cal02_nvt for NVT calculation (Trp-cage)
• cal03_vmcmd for V-McMD calculation (Trp-cage)
• cal04_aus for V-AUS calculation (2 Alanine-pentapeptides)