[AMBER] Setting up parameters for a simulation at 350K

From: Dmitry Suplatov <genesup.gmail.com>
Date: Thu, 4 Oct 2018 18:39:51 +0300

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,



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
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 - 09:00:02 PDT
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