Hi all,
I am a beginner and I would like to simulate an organic molecular crystal (like a Naphthalene organic crystal).
Could you please give me some suggestions about the most suitable force fields? I know that one should first look the literature, but I was not able to find anything useful.
Also, I have the coordinates of the atoms in the unit cell: would you suggest me to input the coordinates in lammps by the lattice command or via the read_data?
Finally: would you be able to provide a sample input file for a similar structure?
Thank you in advance for your help,
Carlo
Hi all,
I am a beginner and I would like to simulate an organic molecular crystal
(like a Naphthalene organic crystal).
Could you please give me some suggestions about the most suitable force
fields? I know that one should first look the literature, but I was not
able to find anything useful.
I guess you didn't look very much. The OPLS-aa FF has been used for this
molecule (at least for liquid phase simulations)
See for example this link:
http://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&ved=0CDwQFjAC&url=http%3A%2F%2Fdigitalcommons.uri.edu%2Fcgi%2Fviewcontent.cgi%3Farticle%3D1005%26context%3Dche_facpubs&ei=EaacUpuhKsaXqQHDt4CwDg&usg=AFQjCNGyOcAyG-ftuKjwpcR9vaDJvCBjVw&sig2=hCpb8jKfqvm9qkY7FNqziQ&bvm=bv.57155469,d.aWM&cad=rja
Now, I don't know if this FF can handle properly the crystalline phase of
your system. Maybe it will as this is a crystal where the structure is set
only by the VDW forces. However, you have to search the publication
repositories to find more about it.
Also, I have the coordinates of the atoms in the unit cell: would you
suggest me to input the coordinates in lammps by the lattice command or via
the read_data?
What does it matter to your overall nutrition if your spoon is metallic or
plastic? Pick the method that is the easiest for you.
Finally: would you be able to provide a sample input file for a similar
structure?
You can build it using your favorite molecular builder software: avogadro
(free), molden (free), material studio ($), and so on... There is a slim
chance a user here will have it ready for you.
Carlos
Hi Carlos,
thank you for your answer.
So if I correctly understand, what you suggest is to check the repository (http://lammps.sandia.gov/papers.html) anf look for similar systems?
Thank you for the paper you suggested. I think that, in order to use that FF, one has to set:
pair_style lj/cut/coul/long 10.5
bond_style harmonic
angle_style harmonic
dihedral_style opls
Sorry for my very naive questions but I come from the ab-initio side and I have really no confidence with MD.
My problems with the geometry input file is that I have not very clear how to set all the Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, and all the numbers related to atoms, bonds, dihedrals, etc...
Regarding the coefficients, I have really no idea how to set them. For the numbers related to atoms, bonds, dihedrals... is there a cheap way to set them/
Thank you again,
Carlo
Ciao Carlo (I’m never sure if with the Italians that ciao is at the entrance or the exit like its is in Spanish),