Overview of sander
input files
Energy Minimisation:
The minimisation input file, sander_min.in
, will include 4000 steps using two different methods: 2000 of gradient descent and 2000 of conjugate gradient. The sander input file looks like this:
Minimisation of system
&cntrl
imin=1, ! Perform an energy minimization.
maxcyc=4000, ! The maximum number of cycles of minimization.
ncyc=2000, ! The method will be switched from steepest descent to conjugate gradient after NCYC cycles.
/
Thermalisation (NVT):
We will use the input file sander_heat.in
to gradually increase the temperature of the system up to our target value over the first 30 ps. To help our system accomodate to this change, we will use a temperature ramp in which we control the temperaure increase per timestep.
Heating ramp from 0K to 300K
&cntrl
imin=0, ! Run molecular dynamics.
ntx=1, ! Initial file contains coordinates, but no velocities.
irest=0, ! Do not restart the simulation
nstlim=15000, ! Number of MD-steps to be performed.
dt=0.002, ! Time step (ps)
ntf=2, ntc=2, ! Constrain lengths of bonds having hydrogen atoms (SHAKE)
tempi=0.0, temp0=298.0, ! Initial and final temperature
ntpr=500, ntwx=500, ! Output options
cut=8.0, ! non-bond cut off
ntb=1, ! Periodic conditiond at constant volume
ntp=0, ! No pressure scaling
ntt=3, gamma_ln=2.0, ! Temperature scaling using Langevin dynamics with the collision frequency in gamma_ln (ps−1)
ig=-1, ! seed for the pseudo-random number generator will be based on the current date and time.
nmropt=1, ! NMR options to give the temperature ramp.
/
&wt type='TEMP0', istep1=0, istep2=12000, value1=0.0, value2=298.0 /
&wt type='TEMP0', istep1=12001, istep2=15000, value1=298.0, value2=298.0 /
&wt type='END' /
Density equilibration (NPT):
The input file sander_equil.in
is used to equilibrate the density of the system for 30ps:
Density equilibration
&cntrl
imin= 0, ! Run molecular dynamics.
nstlim=15000, ! Number of MD-steps to be performed.
dt=0.002, ! Time step (ps)
irest=1, ! Restart the simulation
ntx=5, ! Initial file contains coordinates and velocities.
ntpr=500, ntwx=500, ntwr=500, ! Output options
cut=8.0, ! non-bond cut off
temp0=298, ! Temperature
ntt=3, gamma_ln=3.0, ! Temperature scaling using Langevin dynamics with the collision frequency in gamma_ln (ps−1)
ntb=2, ! Periodic conditiond at constant pressure
ntc=2, ntf=2, ! Constrain lengths of bonds having hydrogen atoms (SHAKE)
ntp=1, taup=2.0, ! Pressure scaling
iwrap=1, ioutfm=1, ! Output trajectory options
/