CHARMM TIP3P

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1

Ok, I got it.

Thanks very much, Axel. But I believe a lot of people did NVT and NPT in this kind of system with LAMMPS.

I have another question here.

For the fluid water, I want to use CHARMM TIP3P rigid water. Then, both sigma and epsilon for H-H and O-H are nonzero. I wrote the ‘Pair Coeffs’ in data file:

Pair Coeffs

1 0.0460 0.4000 (Hydrogen)
2 0.1521 3.15061 (Oxygen)

How can I define sigma and epsilon for O-H? Define them in the input file with ‘pair style’?

I think both of sigma and epsilon are automaticlly calculated by geometric mix rule by LAMMPS which are different with LJ epsilon/sigma of OH for CHARMM TIP3P water model. I am not sure that LAMMPS read ‘Pair Coeffs’ firstly or ‘pair style’?

Thanks,

Hangyan

2011-09-22

2

2011/9/21 physics.hangyan.chen <[email protected]...>:

Ok, I got it.

Thanks very much, Axel. But I believe a lot of people did NVT and NPT in
this kind of system with LAMMPS.

that other people do calculations in an ill defined ensemble,
doesn't make it any more correct. it is quite common that
people misunderstand what npt (or nvt) represent. in a
nanoscale system, there is no bulk that you (can) couple to.

I have another question here.

For the fluid water, I want to use CHARMM TIP3P rigid water.
Then, both sigma and epsilon for H-H and O-H are nonzero. I wrote the
'Pair Coeffs' in data file:

Pair Coeffs

1 0.0460 0.4000 (Hydrogen)
2 0.1521 3.15061 (Oxygen)

How can I define sigma and epsilon for O-H? Define them in the input file
with 'pair style'?

i _never_ place coefficients into the data file. i just find it far
to irritating to have those numbers defined in different locations.

I think both of sigma and epsilon are automaticlly calculated by geometric
mix rule by LAMMPS which are different with LJ epsilon/sigma of OH for
CHARMM TIP3P water model. I am not sure that LAMMPS read 'Pair Coeffs'
firstly or 'pair style'?

you don't define coefficients with pair_style but through pair_coeff.

lammps processes commands in order and later ones override
previous ones. the pair coeffs from the data file are processed when
the data file is read.

axel.