The equilibration should happen in the presence of restraints on the heavy
atoms, reducing the restraints at intervals of 100ps to 1ns until the
protein gets free. Plan on discarding a lot of the initial dynamics. For
a 1000ns run I tend to discard the first 250ns.
Dave
On Thu, Oct 4, 2018 at 1:30 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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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> >
> >
>
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Received on Thu Oct 04 2018 - 11:00:03 PDT
