[gmx-users] Re: Inquiry Again.

Anton Feenstra feenstra at chem.vu.nl
Thu Jul 24 09:15:04 CEST 2003

Victor Kowalenko wrote:
> HI Anton,
> I am a little confused about creating a topology file. When I was doing
> the simulations in MMTK, I had to create special files for Al and Cu
> for the Lennard Jones potential. From what you are saying these will form 
> the topology file for GROMACS. The type of information that was stored
> was the LJ_radius (in Angstroms) and LJ_energy (in eV) for the both atoms.
> Whenever an interaction occurred between an Al and Cu atom MMTK took the
> average of the Al-Al and Cu-Cu interactions. Is that the way GROMACS would
> handle such interactions?

Yes, although there are several ways of 'averaging' the interactions, known
as the 'combination rules'. Check the manual. Also, Gromacs would need
either sigma&epsilon or C6&C12, but that is easy to relate to radius&energy.

> It appears to me that to create a topology file all I need to do is create
> columns of : type (I realise that I might have to add atoms to the .atp
> file), mass, charge (I presume this is the total charge of 0)
> and the paramters epsilon and sigma, which can be obtained from LJ_radius
> and LJ_energy above since these are basically the form given by Eq. (4.5)
> in the reference GROMACS module. Although I know that I must type in 1 to
> specify a Lennard-Jones potential, I believe that I must specify the bonds
> between the atoms under the [bonds] section of the topology file. This may
> give me some degree of lattitude in specifying the Al-Cu interaction 
> that one does not get in MMTK. After this  I presume that I can use the 
> initial pdb file containing the initial coordinates of the atoms in
> the lattice with the *.top file and move on to the next stage of using
> GROMACS by using pdb2gmx to create a structure file so that I can use
> mdrun. Is this correct?

Mostly. You don't need the .atp file, that is only used by pdb2gmx.

You *do* need to add your Cu and Al to the [ atom_types ] section in
your .top file (normally, these would be in one of the forcefield
files for non-bonded parameters, e.g. ffgmxnb.itp). This atom types
section will also contain the L-J parameters as well as the mass.
Charges come in the [ atoms ] section where you define which atoms
(all of them) actually make up your molecule(s) and/or system.

Whether you want/need bonds is up to you to decide. However, it will
have repercussions on how to write your topology. Without bonds,
everything is non-bonded and you can have single atom 'molecules'
of Cu and of Al. You make one molecule type for Cu and one for
Al and then you add as many of these molecules as you need in the
[ molecules ] section.

If you *do* want bonds, your whole system must be one molecule,
since you cannot have bonded interactions between molecules in
Gromacs. Then, you will have an extensive [ atoms ] section in
this 'molecule' type section, defining all of the Cu and Al in
your whole system. Under the [ molecules ] section you will only
include this one 'molecule'.

In both cases, the number of Al and Cu must match with your .pdb
or .gro file, but also the order must be exactly identical. This
means that if Al and Cu alternate in the coordinate file, they
must also alternate in the .top file either like:
[ molecules ]
  Al 1
  Cu 1
  Al 1
(and so on), or like:
[ atoms ]
  1 Al ...
  2 Cu ...
  3 Al ...
(and so on)


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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