about special bonds command in lammps2001

Hi, all:

For the command line “special bonds 0.0 0.0 0.5” in lammps2001, which kind of special_bonds it should be?

Reading the lammps2001 source code, it is not belong to charmm or amber, but corresponds to following:

else
amberflag = 0
special(1) = realread(str,m)
special(2) = realread(str,m)
special(3) = realread(str,m)

Should I choose “special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes”? before the special bonds, I defined the angle style, dihedral style and so on, and I used lj/charmm/coul/long pair_style. Thanks a lot.

Laura

2011/8/28 zhangliqun <[email protected]...>:

Hi, all:

For the command line "special bonds 0.0 0.0 0.5" in lammps2001, which kind
of special_bonds it should be?

Reading the lammps2001 source code, it is not belong to charmm or amber, but
corresponds to following:

else
    amberflag = 0
    special\(1\) = realread\(str,m\)
    special\(2\) = realread\(str,m\)
    special\(3\) = realread\(str,m\)

Should I choose "special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral
yes"? before the special bonds, I defined the angle style, dihedral style
and so on, and I used lj/charmm/coul/long pair_style. Thanks a lot.

how does using "special_bonds charmm" sound?
apparently, you want to simulate a system with
the CHARMM force field, right? please have a look
at the documentation for special_bonds and _read_ it.

cheers,
     axel.

I checked the lammps2001 source code, the special bonds option I used did not use charmm or amber parameters, so it should belong to the third one with contents as I posted. Checking the “special_bonds charmm” in lammps2011, it sets the three parameters to 0.0 0.0 0.0, but my parameters are different from that. That is why I suspect I should use “special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes”.

Laura

2011/8/28 zhangliqun <[email protected]...>:

I checked the lammps2001 source code, the special bonds option I used did
not use charmm or amber parameters, so it should belong to the third one
with contents as I posted. Checking the "special_bonds charmm" in
lammps2011, it sets the three parameters to 0.0 0.0 0.0, but my parameters
are different from that. That is why I suspect I should use "special_bonds
lj/coul 0.0 0.0 0.5 angle yes dihedral yes".

ultimately it is up to you which parameters you use.

the special_bonds documentation explains in detail what to do
to represent a CHARMM force field correctly, including introduction
the 1-3,1-4 interactions as part of the angle and dihedral potential
(since in CHARMM not all dihedrals are scaled the same way,
thus the more complex approach currently).

since lammps 2001 is long considered obsolete,
you cannot expect somebody spending much
effort on trying to reproduce it exactly, including
its (incomplete?) implementations.

just input what you think and see, if you get the
result that you want.

cheers,
    axel.

OK. I will try and see which one is better.

I am working on 343 molecules, each molecule includes 12 atoms. I prepared the data file using MC program. It defined the bond_style parameters which can be used in the “bond_style harmonic” command. But when reading the input file, the lammps2001 gave me error message as following:

Reading data file …
ERROR on proc 0: No bonds allowed with this atom style

I used following settings in the input file:

units real

pair_style lj/charmm/coul/long 10.00 10.10

read_data data.file

bond_style harmonic

what should I do in lammps2011 to do the same kind of simulations? Thanks a lot.

Laura

2011/8/28 zhangliqun <[email protected]...>:

OK. I will try and see which one is better.

I am working on 343 molecules, each molecule includes 12 atoms. I prepared
the data file using MC program. It defined the bond_style parameters which
can be used in the "bond_style harmonic" command. But when reading the input
file, the lammps2001 gave me error message as following:

Reading data file ...
ERROR on proc 0: No bonds allowed with this atom style

I used following settings in the input file:

units real

pair_style lj/charmm/coul/long 10.00 10.10

read_data data.file

bond_style harmonic

what should I do in lammps2011 to do the same kind of simulations? Thanks a
lot.

please pay attention to the error message!

it says that your atom style in not adequate.
since you don't select an atoms style, it will
be set to "atomic" by default. obviously, you
have to select a different atom style. try "full".

lammps comes with a _ton_ of examples,
including examples for charmm based
simulations. before continuing to post a
question at _every_ little stoppage, i recommend
to first spend a little effort looking around and
particularly use some common sense.

axel.