I'd try a small ntpr and ntwx until you know you have it running stable,
for easier debugging if something goes wrong.
Bill
On 10/4/18 8:39 AM, Dmitry Suplatov wrote:
> Dear colleagues,
>
> please comment if any parameters do not seem reasonable for conventional
> MD simulation of a PDB structure at 350K (i.e., a production run after
> EM and EQ) .
>
> Thank you,
>
> Dmitry
>
> -----------------
>
> imin=0, ! Flag to run minimization - No minimization
> irest=1, ! Flag to restart a simulation - Restart the
> simulation, reading coordinates and velocities from a previously saved
> restart file
> ntx=5, ! Option to read the initial coordinates, velocities
> and box size from the inpcrd file - Coordinates and velocities will be read
> nstlim=500000000, ! Number of MD-steps to be performed
> dt=0.001, ! The time step (psec). For temperatures above 300K,
> the step size should be reduced.
> ntc=2, ! Flag for SHAKE to perform bond length constraints -
> bonds involving hydrogen are constrained
> ntf=2, ! Force evaluation - bond interactions involving
> H-atoms omitted (use with ntc=2)
> cut=10, ! The nonbonded cutoff, in Angstroms
> ntb=1, ! Impose periodic boundaries at constant volume
> ntp=0, ! Flag for constant pressure dynamics - No pressure
> scaling
> ntt=3, ! Langevin thermostat
> gamma_ln=2.0, ! Collision frequency in ps−1 for Langevin thermostat
> ig=-1, ! Random seed for Langevin thermostat will be based
> on the current date and time
> temp0=350 ! Reference temperature at which the system is to be kept, if
> ntt > 0.
> iwrap=1, ! The coordinates written to the restart and
> trajectory files will be wrapped into a primary box
> ntxo=2, ! Format of the final coordinates, velocities, and
> box size written to the restart file - NetCDF file
> ioutfm=1, ! The format of coordinate and velocity trajectory
> files - Binary NetCDF trajectory
> ntpr=100000, ! Print the progress of the run to output file every
> ntpr steps
> ntwr=100000, ! Every ntwr steps during dynamics, the “restrt” file
> will be written
> ntwx=100000, ! Every ntwx steps, the coordinates will be written
> to the mdcrd file
> -----------------
>
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Received on Thu Oct 04 2018 - 11:00:02 PDT
