All of these look fine; the time step should be reduced for temperatures in
excess of 300K, but you can probably reduce it according to 0.002fs * 300K
/ [your temperature], and if you are using hydrogen mass repartitioning
then try 0.004fs * 300K / [your temperature]. If you need round numbers
take 1.6fs and collect results every ~15000 steps.
Dave
On Thu, Oct 4, 2018 at 11:40 AM Dmitry Suplatov <genesup.gmail.com> 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
> -----------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 04 2018 - 09:00:03 PDT
