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1

Dear All

I am performing a simulation of 108 water molecules using Lammps- Nov 10 version.
I simulated the system for Ins in NPT ensemble followed by another run in NVT at
300K. Assuming the system to have equilibrated, I started NVE run for 5ns but
the system temperature immediately fell to 200K.

I am not able to figure out, why my system doesn’t undergoes equilibration.I am attaching the
the input file and log files(of NPT and NVT run) for your kind consideration.
dimension 3
units real
boundary p p p

kspace_style ewald 1.0e-4

kspace_modify order 3
atom_style full
pair_style lj/cut/coul/long 11.0
bond_style harmonic
angle_style harmonic
pair_modify mix arithmetic
newton off
read_data water_108.lammps05
#read_restart xfile.restart.100000
group cat type 1
group ain type 2
group wtr type 1 2
#variable fff equal fx[1]
neighbor 1.0 bin
neigh_modify delay 0 every 1 one 6000
minimize 1.0e-4 1.0e-6 100 1000
fix 1 wtr shake 0.0001 20 0 t 1 2 a 1 b 1
fix 2 all npt temp 300.0 300.0 100.0 iso 1.00 1.00 1000.0 drag 0.3
#fix 3 all temp/rescale 10000 300.0 300.0 0.005 1.0
compute ab all rdf 200 1 1 1 2 2 2
compute bc all msd com yes
fix 3 all ave/time 100 1 100 c_ab file rdf.out mode vector
fix 4 all ave/time 100 1 100 c_bc file msd.out mode vector

fix 2 all nve

timestep 1.0

thermo 10000
thermo_style custom step pe ke etotal temp press vol

restart 50000 z.restart

dump 1 all custom 100 z.output.dump id type efieldx efieldy efieldz
dump 2 all custom 100 z1.output.dump id type x y z
run 1000000

Thanks In Advance…
DeepaK Ojha
School Of Chemistry

“Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live”

log.lammps (12.7 KB)

log.lammps (6.33 KB)

2

First, I would use the current LAMMPS. Many
bugs may have been fixed in 1.5 years.

Second, I would make sure the temperature you are
calculating and displaying is accounting for the
degrees of freedom that SHAKE is removing. E.g.
try running w/out SHAKE and see what the temperature
does.

Steve

3

Dear All

I am performing a simulation of 108 water molecules using Lammps- Nov 10
version.
I simulated the system for Ins in NPT ensemble followed by another run in
NVT at
300K. Assuming the system to have equilibrated, I started NVE run for 5ns
but
the system temperature immediately fell to 200K.

this is a self-inflicted problem. if you want to continue
cleanly, you *must* not do a minimization. that will
*undo* most of the effect of the equilibration with fix
nvt. furthermore, during minimization velocities are
not used but carried over, but the degrees of freedom
that are removed by fix shake are added back, hence
the drop to ~200K (shake on water removes 3 out of
9 degrees of freedom).

that the low temperature carries over to the subsequent
MD, is not due to that, but rather due to the *potential*
energy that was removed during the minimization.

I am not able to figure out, why my system doesn't undergoes
equilibration.I am attaching the
the input file and log files(of NPT and NVT run) for your kind
consideration.

this is fairly straightforward to see.
you have to be much more careful
with your simulation protocol.

axel.