- Syntax
build <subcommand> [arguments]
- Subcommands and examples:
- mdCore/core
- To build MD core from current structure and control parameters, and pack a compact force filed parameters needed for further MD simulation. And the MD core can be save to a file for further usage, please see command "saveMDS" and "loadMDS".
# do a build a MD core
buildcore timestep=0.002 nstep=1000000 nprint=100 \
trjfile="step9_harvest.trj" frqtrj=500 trjfmt=movar \
rstfile="step9_harvest.rst" frqrst=10000 \
enefile="step9_harvest.ene" frqene=100 \
randseed=314159 randtype=old \
frqresort=20000
#load last coordinates and velocities
loadstate file="step8_equil_npt.rst" coordvelonly=true
#save whole MD system setup to a compact binary file
savesetup file="step9_harvest.mds"
- Arguments
integrator=<type name>
Tell the integration type, available types are:
Leapfrog
the default value
Vverlet
velocity verlet integrator
timestep=<real>
To tell the time step for integration
nstep=<int>
To tell the total number of MD step to run, which can be changed by command "mdcp" or can be reassigned in command "runmd".
nprint=<int>
To tell how frequency to print energies to log file
Trjfile=<filename>
To tell the trajectory file name.
Frqtrj=<int>
To tell how frequency to save a frame to trajectory file
FrqNewTrj=<int>
The trajectory will be stored to new file with a MD step mark in file name for every FrqNeqTrj number steps, the default is 0 means no splitting strategy.
Trjfmt=<type name>
To tell the trajectory file format, only Modar or CHARMM available currently
Rstfile=<filename>
To tell the restart state file name
Frqrst=<int>
To tell the frequency for saving system state (Restart state file) for resuming run
Enefile=<filename>
To tell the energies profile file name
Frqene=<int>
To tell the energies profile write out frequency
Frqresort=<int>
To tell how frequency to do coordinates resorting; this does save time for reducing random memory accessing.
Randseed=<int>
To initiate the random seed
Randtype=<type name>
Old or New, default value is Old.
Flushlog=<bool>
Flush log file or not, default value is false
Flushene=<bool>
Flush ene file or not
Flushtrj=<bool>
Flush trj file or not
- To build MD core from current structure and control parameters, and pack a compact force filed parameters needed for further MD simulation. And the MD core can be save to a file for further usage, please see command "saveMDS" and "loadMDS".
- top
- To rebuild molecular topology in to force filed interpretation. Modar can builds molecular topology automatically when loading a structure file. However, the initial structure loaded may not be described properly due to some nomination, we need to make some revision and then call this command to build the topology.
# build solute topology from
Build top
- Arguments
none
- To rebuild molecular topology in to force filed interpretation. Modar can builds molecular topology automatically when loading a structure file. However, the initial structure loaded may not be described properly due to some nomination, we need to make some revision and then call this command to build the topology.
- mdCore/core
- unkcrd
- To rebuild coordinates for atoms whose coordinates haven’t been initiated yet according to force field description.
# build coordinates not initiated yet
Build unkcrd
# replace Hydrogen atoms
Atom resetcrd select=¡±name H*¡±
Build unkcrd
- Arguments
none
- To rebuild coordinates for atoms whose coordinates haven’t been initiated yet according to force field description.
- Variables exported
none
Contact us
| Phone: | 400-660-8656 | |
| Email: | support@beemd.org |
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