Dear All users
I wanted to do npt ensemble but pressure and temperature of my system fluctuated too much, by this reason I decide use these command before doing npt:
fix 1 all langevin 200.0 420.1 1.0 36
fix 2 all nve
fix 3 all press/berendsen iso 0.0 1.0 10.0
But I like starting my traj from step o in the second run, my total command :
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. dump 1 all atom 1000 traj_npt.trj
thermo 1000
thermo_style custom step temp pe press vol
minimize 1.0e-5 1.0e-7 100000 100
(Note: Some fixes, for example “shake”, interfere with the minimize command,
You can use the “unfix” command to disable them before minimization.)
– declare time step for normal MD –
timestep 0.00001
fix 1 all langevin 200.0 420.1 1.0 36
fix 2 all nve
fix 3 all press/berendsen iso 0.0 1.0 10.0
– Now, finally run the simulation –
run 10000
unfix 1
unfix 2
unfix 3
undump 1
– run at constant pressure (Nose-Hoover)–
dump 2 all atom 1000 traj_npt.trj
log npt.log
compute 1 all rdf 10 1 1
compute 2 all rdf 10 2 2
compute 3 all rdf 10 1 2
compute mytemp all temp
compute mypress all pressure mytemp
fix 4 all store/force
fix fxnpt all npt temp 420.0 420.0 1.0 iso 1.0 1.0 10.0
fix 5 all ave/time 100 1 100 c_1 c_2 c_3 file tmp1.rdf mode vector
fix 6 all ave/time 100 1 100 c_mypress c_mytemp file tmp1.pt
run_style verlet
run 10000 start 0
print “All done”