Dear David,
thank you for fast response. I am actually a fan of your FF15IPQ set,
the results are indeed more interesting compared to FF14SB which tends
to over stabilize the protein.
Could you also have a quick look at parameters for simulation in NPT and
350K (my equilibration template).
Thanks, 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=42500, ! 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=2, ! Impose periodic boundaries at constant pressure
ntp=1, ! Flag for constant pressure dynamics - md with
isotropic position scaling
taup=2.0, ! Pressure relaxation time (in ps), when NTP > 0. The
recommended is [1 - 5]. (use larger values to disturb Newton's equations
as little as possible)
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=10000, ! Print the progress of the run to output file every
ntpr steps
ntwr=10000, ! Every ntwr steps during dynamics, the “restrt” file
will be written
ntwx=10000, ! Every ntwx steps, the coordinates will be written to
the mdcrd file
-------
On 10/4/18 6:45 PM, David Cerutti wrote:
> 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
> <mailto: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
> -----------------
>
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Received on Thu Oct 04 2018 - 09:30:02 PDT
