Dear LAMMPS users,
I am facing a problem of energy conservation. Let me explain my problem first.
I took a big water box and performed NPT at 300 K-1 atm . Then i performed NVT at 300 K. I believe that my system is in equilibrium at 300 K. All the simulations were performed with PBC.
I cut a sphere of water molecules from this equilibriated water box and also the velocity of those water molecules. Now I am performing NVE on this spherical water without using minimize command in a very large box size. I am finding that temperature/total energy of this spherical set of water molecules falls very quickly within few fs. I think energy should remain constant in the system while NVE. Why does temperature fall within few fs even water cluster has not even expand?
I will be very thankful if anyone can suggest something regarding this.
regards-
That seems weird. The total energy of the system should be conserved if fix nve is the only time-integrating fix for all your particles.
Your description is not very clear to me though. Do you mean that you equilibrate water in a box and then take out a spherical region and use that as input for a new simulation? Or is the rest of the system still there but is it no longer being integrated? I can imagine that if you monitor only the temperature of the water inside this region but they interact with the other particles in the box, they can transfer their kinetic energy to the rest of the system which you would measure as a drop in temperature.
Can you post your input script and data file(s)?
Dear LAMMPS users,
I am facing a problem of energy conservation. Let me explain my problem
first.
I took a big water box and performed NPT at 300 K-1 atm . Then i performed
NVT at 300 K. I believe that my system is in equilibrium at 300 K. All the
simulations were performed with PBC.
I cut a sphere of water molecules from this equilibriated water box and
also the velocity of those water molecules. Now I am performing NVE on this
spherical water without using minimize command in a very large box size. I
am finding that temperature/total energy of this spherical set of water
molecules falls very quickly within few fs. I think energy should remain
constant in the system while NVE. Why does temperature fall within few fs
even water cluster has not even expand?
difficult to say without knowing more details, but you have made a
*massive* change to your system's potential energy landscale. for all
the water molecules in your sphere, and particularly those close to
the surface, you have removed a *lot* of their neighbors and thus
massively changed their interactions and their potential energy.
this kind of system will need to be reequilibrated, because it will
experience significant restructuring on the surface and a buildup of
surface tension and so on. check out the literature on MD simulations
of water (and other liquid) droplets
to rationalize this, of two particles connected with a spring in a
harmonic oscillator. assume the spring between those two particles is
extended close to the turning point and suddenly you remove one of the
two particles. what will happen?
axel.
Dear Stefan,
Thank you so much for your response. Yes, i equilibrated water in a box and then cut out a spherical region. Then NVE was performed only on this spherical water cluster in a large box. Velocity of these waters was also taken from equilibriated system. Rest of the system was not present there anymore. I performed NVE on spherical water cluster with velocities at 300K in a large box. I hope i am clear now. Here i am providing my script.
dimension 3
units real
boundary p p p
kspace_style pppm/tip4p 1.0e-4
kspace_modify order 3
atom_style full
pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 15.0
bond_style morse
angle_style harmonic
pair_modify mix arithmetic
read_data FilledConfig.data
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes page 100000
fix 2 all nve
timestep 1.0
thermo 1
thermo_style custom step temp press vol pe ke etotal
restart 500 h2o.restart
dump 6 all custom 1 h2o-pos.dump id type x y z
dump 7 all custom 1 h2o-vel.dump id type vx vy vz
run 1500 start 0
I hope for some solution.
Thank you so much
regards-
Pankaj Mishra
Dear Stefan,
Thank you so much for your response. Yes, i equilibrated water in a box and
then cut out a spherical region. Then NVE was performed only on this
spherical water cluster in a large box. Velocity of these waters was also
taken from equilibriated system. Rest of the system was not present there
anymore. I performed NVE on spherical water cluster with velocities at 300K
in a large box. I hope i am clear now. Here i am providing my script.
dimension 3
units real
boundary p p p
kspace_style pppm/tip4p 1.0e-4
kspace_modify order 3
atom_style full
pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 15.0
bond_style morse
angle_style harmonic
pair_modify mix arithmetic
read_data FilledConfig.data
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes page 100000
fix 2 all nve
timestep 1.0
you do a 1fs time step without shake?
that is not likely to conserve energy even with PBC and deuterated water.
have you tried running your bulk system with nve?
the remarks i made about cutting out a system go on top of all of this.
axel.