hbond/dreiding/lj

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1

Hi Lammps users,

I have set up a system with dreiding force field, I need to verify following statement.

pair_coeff 3 4 hbond/dreiding/lj 5 j 9.0 2.75 4

where Atom type 3 is acceptor, 4 is donor, 5 is hydrogen atom,

In manual page, its given as K = hydrogen atom type = 1 to Ntypes

whether K value specified by me is correct?

Thanks in advance

Karteek Kumar

2

Hi Lammps users,

I have set up a system with dreiding force field, I need to verify following
statement.

pair_coeff 3 4 hbond/dreiding/lj 5 j 9.0 2.75 4

   where Atom type 3 is acceptor, 4 is donor, 5 is hydrogen atom,

For one thing, in your pair_coeff statement is incomplete.
You need to specify 3 more numbers:

distance cutoff Rin (distance units)
distance cutoff Rout (distance units)
angle cutoff (degrees)

In manual page, its given as K = hydrogen atom type = 1 to Ntypes

whether K value specified by me is correct?

K should be the atom type number which corresponds to your hydrogen atom.

--- "i" or "j" ? ---

pair_coeff 3 4 hbond/dreiding/lj 5 j 9.0 2.75 4

   where Atom type 3 is acceptor, 4 is donor, 5 is hydrogen atom,

According to the documentation pate, if 4 is the donor, then the "j"
(in "5 j") is correct. (At least that's the way I understand it. If
you are worried this is not the case, then edit the
"pair_hbond_dreiding_lj.cpp" file, and add some printf statements in
the compute() function which print out the type of the hydrogen atom.
I can't give you more explicit instructions because I don't have
stable computer access right now.)

As always, let us know if you find a bug.

Andrew

3

Thanks Andrew for the reply,

In documentation, I was confused with below statement.

" If the donor flag is i, then the atom of type I in the pair_coeff command is treated as the donor, and J is the acceptor. If the donor flag is j, then the atom of type J in the pair_coeff command is treated as the donor and I is the donor"

In the above line, donor flag is j, both I & J are specified as donor.

Second thing, I didnt specified distance and angle cutoff in pair_coeff to use same as global cut off.

Now, I am unable to equilibrate a system with hbond/dreiding/lj. Total energy drifts continuously.

Please find some test files as attached.

Thanks in advance,

Karteek Kumar

test.tar (50 KB)

4

Hi Andrew,

I tried to equilibrate methanol system given in examples directory. Even that didnt helped me.

  1. I tried with same files in NVE ensemble, total energy drifts ( not sure why?)

  2. Again with NVT ensemble,

fix 2 all nvt temp 300.0 300.0 100.0
fix 2 energy yes

Total energy drifts again.

But surprisingly, If I comment out fix_modify energy yes, Total energy remains constant.

Please can you look into these things.

Thanks

Karteek Kumar