1. System Preparation¶
Author: | Kota Kasahara |
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1.1. Input files¶
The input files required for MD simulations by omegagene are compatible with myPresto/psygene. omegagene requires
- Restart file (including the initial coordinates and velocities)
- Topology file (generated by Tplgene program)
- Shake file (generated by SHAKEinp program)
In addition, two configuration files are required.
- System configuration file (system.cfg)
- Simulation configuration file (md.cfg)
omega_toolkit generates a binary file by combining some of the input files.
python2.7 ${OMEGATK}/mdinput_generator.py -i system.cfg -o system.cls
Example of system.cfg file is shown below:
system.cfg:
--fn-i-tpl et1.tpl ; Topology file
--fn-i-initial-pdb et1.pdb ; Structure file in .pdb format
--fn-i-restart et1.restart ; Restart file
--cell-x 61.2425 ; Specifying the each length of cell-axes
--cell-y 61.2425
--cell-z 61.2425
--fn-i-shake system.shk ; SHAKE file
;--fn-i-ttp-v-mcmd-inp ttp_v_mcmd.inp ; For V-McMD
;--fn-i-ttp-v-mcmd-initial start.vert ; For V-McMD
md_input.cfg:
--mode md ; Only the keyword "md" is accepted
--integrator leapfrog-presto ; "leapfrog-presto" or "zhang"
--thermostat scaling ; Thermostat algorithm
; "none" or "scaling"
--cutoff 12.0 ; Cutoff distance in angestrome
--n-steps 10 ; The number of steps to be calculated
--time-step 2.0 ; Integration time step in fs
--electrostatic zero-dipole ; Only "zero-dipole" is accepted for GPU
; "zero-quadrupole", "zero-octupole", and
; "zero-hexadecapole" are also aceppted for CPU.
--ele-alpha 0 ; Dumping factor for ZD
; only 0 is OK for GPU version
--temperature 300 ; The target temperature
;--temperature-init 10 ; The initial temperature
;--heating-steps 10000 ; The number of steps for heating
--print-interval-log 1 ; Interval steps for printing logs
--print-interval-coord 1 ; Interval steps for output the trajectory
--fn-o-coord trpc.trr ; File name for the output trajectory
--format-o-coord presto ; File format for the output trajectory
; only "presto" is allowed.
;--fn-o-log et1.log ; Not used in the current version
;--fn-o-energy et1.ene ; Not used in the current version
--nsgrid-cutoff 13.0 ; Neighbor search cutoff radius (angstrom)
--nsgrid-update-intvl 50 ; Interval time steps for update the neighbor search grid
; Expanded ensemble
;--expanded-ensemble v-mcmd ; "none", "v-mcmd", or "v-aus"
;--fn-o-vmcmd-log ttp_v_mcmd.out ; Output filename
;--fn-o-expand-lambda mule.ene ; Output filename
;--print-interval-expand-lambda 1 ; Interval steps for the output
;--format-o-expand-lambda ascii ; "ascii", or "binary"
1.2. Execute¶
omegagene executes a MD simulation with two configuration files provided as command line arguments. The current version of omegagene output log messages to the standard output. Redirecting to a log file is recommended.
omegagene --inp et1.cls --cfg md_input.cfg > log.txt