Incorrect degree of freedom for Gay-Berne spheroid that unable to fix

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Dear LAMMPS experts,

I’m using LAMPPS for the Gay-Berne uniaxial ellipsoidal particles to simulate Smectic-A liquid crystals. But I found that the density of the system cannot converge to the correct value even I manually set the degree of freedom of the particles.

The problem is that, the default degree of freedom (DOF) for Gay-Berne model in LAMMPS was set to be 6 (three translational and three rotational DOF). While I believe that the DOF for my uniaxial ellipsoidal particles should be 5.

Hence, when I use NpT/asphere ensemble to equilibrate the system without changing DOF, the average temperature calculated was six fifths of the value I set and, the pressure and density was also wrong because of that. The input file “Input_no_change_of_DOF” for this simulation is attached below.

However, when I manually set the DOF to be 5, I can get the correct temperature and pressure but the density I get is still the same wrong value as before. Hence I suspect that the system did not change the DOF in the integration loop but only change the DOF when calculating the output p and T. The input file “Input_DOF_changed” is also attached below. Currently I have no idea how to fix this thus I need a bit of help.

It is most appreciated if you could provide any suggestions or spot anything wrong in my input file.

Below are the two input files attached.

“Input_no_change_of_DOF”

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Hence I suspect that the system did not change the DOF in the integration loop but only change the DOF when calculating the output p >
and T.

Two things.

This line: compute_modify thermo_temp extra 1

is not subtracting 1 extra DOF for each ellipsoid, only

for the entire system. You would need to set it to N,

where N = # of ellipsoids.

You also need to insure that fix npt/asphere is using the

same adjusted thermostat to compute its pressure,

which it won’t be default. You need to use the

fix modify command, with its temp and/or press

keywords. See the fix npt doc page for details

of how to do this. In your thermo output you

can print out the pressure that fix npt is using,

to insure it is the same correct pressure (or temp)

that your adjusted DOF compute is using.

Again see the fix npt doc page.

Steve