using GROMOS in LAMMPS

LAMMPS LAMMPS Mailing List Mirror
1

Dear all,

I am a beginner in using LAMMPS. I nearly know how to simulate a biopolymer with LAMMPS. For this end, one would use CHARMM force field and ch2lmp toolbox that comes with LAMMPS.

Now, I want to simulate a synthetic polymer. It is an alkane chain and I know that I should use the GROMOS force field. Is there any easy way to use GROMOS force field in LAMMPS? I mean a toolbox similar to ch2lmp that generates in and data files?

Any idea about simulating alkanes with LAMMPS will be helpful to me

Many thanks in advance,

Narges Nikoofard

2

Dear all,

I am a beginner in using LAMMPS. I nearly know how to simulate a biopolymer
with LAMMPS. For this end, one would use CHARMM force field and ch2lmp
toolbox that comes with LAMMPS.

please note that ch2lmp only supports very old charmm force fields (up
to 22 or so, perhaps 27, if you don't use cross terms).

Now, I want to simulate a synthetic polymer. It is an alkane chain and I
know that I should use the GROMOS force field. Is there any easy way to use
GROMOS force field in LAMMPS? I mean a toolbox similar to ch2lmp that
generates in and data files?

no. moreover, it is likely not needed. all that is needed is the
topology information (what bonds go where and what angles, dihedrals
etc.) and then which partial charges need to be assigned. for
biopolymers, you can use some kind of heuristics to build this, since
you have only a small number of identical templates (amino acids). for
other polymers, there are many more possible ways how things are
connected and how they need to be parameterized, so that the heuristic
approach is not as simple (although both charmm and amber have a
"generic force field" that is compatible with the rest. however those
parameters often need to be tweaked and optimized. to be reasonably
accurate).

Any idea about simulating alkanes with LAMMPS will be helpful to me

i have been using OPLS/AA with alkanes and a recipe to write scripts
in VMD/Tcl script to build such topologies for lammps are here:

https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2

of course, those come with the usual warning, that they can eat up
your disk drive if you are not careful and know what you are doing.
but the latter is a pre-requisite for meaningful research anyway.

axel.

3

Look into Towhee: http://towhee.sourceforge.net/towhee_capabilities.html

It is free and has support for the Gromos FF (at least one) and some of the Charmm FFs as well. Towhee has a built in molecule assembler and can generate input files for lammps (mind you that not all FFs are supported when converted to lammps format). Anyways, worth taking a look at it. Your future Towhee questions should go then to the Towhee mailing list.

Carlos

4

And there is a pair lj/gromacs and pair lj/gromacs/coul/gromacs

for the GROMOS pair interactions with its smoothing function.

Steve

5

The "moltemplate" molecule builder can be used to quickly create
LAMMPS data files and input-scripts for arbitrary small organic
molecules.

It already automatically generates force-field parameters according to
AMBER GAFF conventions. However, thanks to Jason Lambert, moltemplate
can automatically assign force-field parameters and charges using
OPLSAA conventions (in addition to automatically generating angle,
dihedral, and improper interactions, as before). This is a relatively
simple process:

1) Create a file which defines a molecule in moltemplate (.lt) format.
The atoms in that file should use OPLSAA atom name conventions. (See
"ethylene.lt" file attached for a simple example.)

2) Edit "oplsaa.txt" file to delete atoms (lines beginning with the
word "atoms") which you don't need in your simulations. Then save the
new file as "oplsaa_subset.txt"

3) Run Jason Lambert's "oplsaa_moltemplate.py" script:
./oplsaa_moltemplate.py oplsaa_subset.txt

4) Run moltemplate:
moltemplate.sh system.lt

I have attached a complete example of how to set up a simulation ethylene gas.

I also attached the latest version of moltemplate.sh (v1.19), which
you will need. (Copy that file to the "src" directory where you
currently have moltemplate.sh.) In the near future, all of these
files will be included automatically with moltemplate. (Newer
versions will contain corrections, so in the future, please look in
the moltemplate/tools directory instead of using the files attached
this post.)

Note: The OPLSAA implementation in moltemplate currently uses
pair_style lj/cut/coul/long 10.0 10.0

If this is not appropriate for OPLSAA, please let me know...

Disclaimer: This code, and this example was just created recently and
(apart from a short simulation which did not crash), we have not
tested it rigorously for accuracy.
As always, please let us know if there are bugs.

Cheers!
(Thanks to Jason for volunteering his code!)

Andrew

ethylene_2013-4-01.tar.bz2 (147 KB)

moltemplate.sh.bz2 (12.5 KB)

ethylene.lt (1.5 KB)

system.lt (511 Bytes)