Dear LAMMPS users ,
Greetings .
I want to convert CG-C60 with MARTINI force field that I have attached with this Email to LAMMPS data format .
One section of this force field is improper dihedrals ( the last section of the file ) , can I use it as improper section of LAMMPS data file ?
Actually at this force filed instead of Dihedral and improper separately there is just " improper dihedrals " .
I appreciate your opinions in advance.
Best Regards.
Saeed
1.itp (19.5 KB)
I want to convert CG-C60 with MARTINI force field that I have attached with
this Email to LAMMPS data format .
Hmm. I did not realize somebody made a MARTINI-compatible model of a
C60 fullrene.
Unfortunately, nobody has yet written a program to automatically
convert ".itp" files into LAMMPS data files. I think Saeed Bashusqeh
converted the .itp file by hand when he created the MARTINI example
shown on the www.moltemplate.org web page.
If you want to write such a converter, I can help. I just don't
know the format of the various .itp files very well.
Actually at this force filed instead of Dihedral and improper separately
there is just " improper dihedrals " .
I strongly suspect this means "impropers" (ie not "dihedrals")
(I am guessing that a C60 fullrene or a graphene does hot have any
ordinary dihedrals.)
One section of this force field is improper dihedrals ( the last section of
the file ) , can I use it as improper section of LAMMPS data file ?
I'm sure that one of the improper_styles available in LAMMPS is
capable to simulate the improper forces in the C60 molecule. Check
out:
http://lammps.sandia.gov/doc/improper_style.html
http://lammps.sandia.gov/doc/Section_commands.html#comm
However, the "[improper]" section of the .itp file you attached
("1.itp") has a different format than the format understood by LAMMPS,
and the atom-order may be different as well. I suspect that the paper
that explains the model explains the kind of improper interactions you
should use (including the formula for the improper energy): Have you
read the paper?
http://perso.ibcp.fr/luca.monticelli/MARTINI/index.html
Pick an improper_style which most closely matches the formula used
in the paper. Keep in mind that the order of the atoms in the
improper interaction matters. Impropers listed in the "1.itp" file
may use different atom order than what LAMMPS is expecting. The most
important thing is to figure out which of the 4 atoms is the central
atom.
Good luck.
Andrew
I want to convert CG-C60 with MARTINI force field that I have attached with
this Email to LAMMPS data format .Hmm. I did not realize somebody made a MARTINI-compatible model of a
C60 fullrene.Unfortunately, nobody has yet written a program to automatically
convert ".itp" files into LAMMPS data files. I think Saeed Bashusqeh
converted the .itp file by hand when he created the MARTINI example
shown on the www.moltemplate.org web page.
If you want to write such a converter, I can help. I just don't
know the format of the various .itp files very well.Actually at this force filed instead of Dihedral and improper separately
there is just " improper dihedrals " .I strongly suspect this means "impropers" (ie not "dihedrals")
(I am guessing that a C60 fullrene or a graphene does hot have any
ordinary dihedrals.)
Actually I looked at the "1.itp" file you attached more carefully, and
I think I was wrong about this. Perhaps they are dihedrals (between 4
consecutively bonded carbons). It is not clear to me from reading the
file.
Are the 4 atoms in the 4-body improper interactions consecutively
bonded togehter? Or is one atom in the center, and the other 3 are
bonded to it?
Again, the best way is to look at the paper and see how they define these.
One section of this force field is improper dihedrals ( the last section of
the file ) , can I use it as improper section of LAMMPS data file ?I'm sure that one of the improper_styles available in LAMMPS is
capable to simulate the improper forces in the C60 molecule. Check
out:http://lammps.sandia.gov/doc/improper_style.html
http://lammps.sandia.gov/doc/Section_commands.html#commHowever, the "[improper]" section of the .itp file you attached
("1.itp") has a different format than the format understood by LAMMPS,
and the atom-order may be different as well. I suspect that the paper
that explains the model explains the kind of improper interactions you
should use (including the formula for the improper energy): Have you
read the paper?
http://perso.ibcp.fr/luca.monticelli/MARTINI/index.html
Pick an improper_style which most closely matches the formula used
in the paper. Keep in mind that the order of the atoms in the
improper interaction matters. Impropers listed in the "1.itp" file
may use different atom order than what LAMMPS is expecting. The most
important thing is to figure out which of the 4 atoms is the central
atom.
I forgot to add that the improper topology goes in the "Impropers"
section of a LAMMPS data file (or the "Data Impropers" section of a
moltemplate .lt file.) The format is described in
http://lammps.sandia.gov/doc/read_data.html
--- Exerpt: ---
"Impropers section:
one line per improper
line syntax: ID type atom1 atom2 atom3 atom4
ID = number of improper (1-Nimpropers)
type = improper type (1-Nimpropertype)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
example:
12 3 17 29 13 100"
Dear LAMMPS users ,
Greetings .
I want to convert CG-C60 with MARTINI force field that I have attached with
this Email to LAMMPS data format .One section of this force field is improper dihedrals ( the last section of
the file ) , can I use it as improper section of LAMMPS data file ?
this is a confusing question. what exactly are you asking here?
whether improper dihedrals and impropers are the same??
Actually at this force filed instead of Dihedral and improper separately
there is just " improper dihedrals " .
this is a file specific to gromacs, thus you should read (and
understand!) the gromacs documentation and particularly its file
format.
and then you can translate/adapt the file as needed.
axel.