-vl <number>

for declare verbose level, default value is 0, bigger means louder

-np <number>

for declare the # of threads for OpenMP.

Modar can detect # of cores available automatically

So you don't need to set this opt if you have no idea

-o <log file>

to tell the log file name, by default,  Modar will create a log file using the same filename of input

-s

to print log message to screen rather than to the default log file

-flush

to enable instant flushing for output/log file

-debugdumb

to tell debug dumping file path, for debug only

-repm

to enable Replica Exchange Simulation rather than parallel

-shm

to enable share memory for MPI communication

-dd

to enable domain decomposing method for parallel dividing, this is the default parallel dividing method used in MoDaR

-fftd

to use FFT decomposing method parallel dividing

-spcd

to enable spatial decomposing method for parallel dividing

-tabnp <number>

or -tabscale <number>

to set # of control points per angstrom for spline interpolation, default value is 100, which is good enough for approximation

-notab

to disable lookup table for all case, by default lookup table is alway on for Ewald terms for CPU base          while for GPU base, the default value is false, and it also turns nonbonded optimization off

-nonbopt

to disable nonbonded optimization

-nnbopt <number>

to set total # of atomtype for nonbonded optimization, default value is 20, which is enough for most system

-nobak

to disable file backup, MODAR backups all files existed by default, backup function will be disabled for restart case

-nohts

to disable termination signal handling policy,          MODAR handles termination signals internal by default,          use this flag to turn off the handling policy

-restart

to enable continuously restarting write out,              rather than to create new files, see following -mds -rst -nstep –nstepmore, for more detail about to do a restart MD run

-mds <mds file>

the Modar .mds file, i.e. the whole MD system setup packed in a binary file

-rst <rst file>

the Modar restarting state in a binary file

-nstep <number>

the total step MD will run

-nstepmore <number>

the number of step MD will be continued

Modar can detect file format automatically, for instance, to launch a 1ns more restart run simply by command:

./modar -restart run.mds run.rst -nstepmore 500000 -o more_1.log

-v

to print version information

-h

to print this manpage

-cuda <on/off>

To enable/disable CUDA GPU speedup for cuda build only