Run Simulation (DL_POLY)¶
This page is related to the tutorial section to setup a solution model using DL_FIELD. If you have not done so, please go to Setup solutions.
If you have run the simulation and produced a HISTORY trajectory file, you can proceed to Atomic Interaction Analysis Using D_ATA.
Otherwise, please continue on the tutorial as follows:
The FF structure obtained from DL_FIELD would need to be equibrated before taking the sample and write to HISTORY trajectory files. For this tutorial, we will carry out sampling run at 300 K and 1 atm pressure.
Below shows several runs, each using the CONFIG file from the previous run to the next.
Note
You can use up to 4 processors to run these simulations. To reduce simulation time, you can reduce total timesteps, say, from 10000 steps to 5000 steps.
Procedures
‘Equilibration’. Strictly speaking, this step is taken to ‘unlock’ any structures that are in highly energetic conformations. This can occur, as for instance, DL_FIELD places solvent molecules in some unfavourable orientations with respect to solutes. Use the following CONTROL file:
Run 1: Resolve any high-energy conformation
ensemble nve
zero
cap 5000.0
densvar 20
steps 2000
equilibration steps 1000000
scale every 1
timestep 0.002
cutoff 12.000000
ewald precision 1e-6
mxshak 100
shake 1.0e-5
job time 100000
close time 200
finish
Remember to use the final configuration (REVCON) for the next simulation run below.
Equilibration in NVE ensemble, rescale temperature to 300 K at every timestep, for a total of 10,000 steps. The timestep is set to 0.002 ps. Use the following CONTROL file.
Run2: Equilibration at NVE
ensemble nve
temperature 300.0
densvar 20
steps 10000
equilibration steps 1000000
scale every 1
timestep 0.002
cutoff 12.000000
ewald precision 1e-6
mxshak 100
shake 1.0e-5
stats every 1000
print every 1000
job time 100000
close time 200
finish
The use of restart noscale directive means reset the time to zero and use the initial velocities as defined in the CONFIG file.
Remember to use the final configuration (REVCON) for the next simulation run below.
Equilibration in NPT ensemble, by using hoover as the thermostat and barostat and set the temperature to 300 K and 1 atm, respectively. Use the following control file.
(3) Equilibration at NPT.
ensemble npt hoover 0.4 1.0
pressure 0.00101325
temperature 300.0
densvar 20
steps 10000
equilibration steps 0
scale every 1
timestep 0.002
cutoff 12.000000
ewald precision 1e-6
mxshak 100
shake 1.0e-5
restart noscale
stats every 1000
print every 1000
job time 100000
close time 200
finish
Remember to use the final configuration (REVCON) for the next simulation run below.
Sampling run in NPT ensemble, as before. This time, a directive traj 0 200 0 is used to instruct DL_POLY to create a HISTORY trajectory file and write out the atomic configuration every 200 steps. Use the following CONTROL file.
Run 4: Sampling run at NPT
ensemble npt hoover 0.4 1.0
pressure 0.00101325
temperature 300.0
densvar 20
steps 10000
equilibration steps 0
scale every 1
timestep 0.002
cutoff 12.000000
ewald precision 1e-6
mxshak 100
shake 1.0e-5
restart noscale
traj 0 200 0
stats every 1000
print every 1000
job time 100000
close time 200
finish
Congratulations, you have created a HISTORY trajectory file! If you want to analyse atomic interactions, you can proceed Atomic Interaction Analysis Using D_ATA.