[gmx-users] Re: Inquiry Again.

Victor Kowalenko victork at mail.csse.monash.edu.au
Wed Jul 23 12:10:01 CEST 2003

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?

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?

Victor Kowalenko.    

On Fri, 18 Jul 2003, Anton Feenstra wrote:

> Victor Kowalenko wrote:
> > I was a little the pdb2gmx might be restricted to only molcular
> > applications. Your option of adjusting the topology file manually
> > might be superior. Again I will look into this on Monday.
>  From your description, it sounds as if you may only need Lennard-Jones
> potential interactions, in which case it is fairly trivial to write the
> Gromacs topology with your parameters. If you need bonded interactions
> (that is, e.g. harmonic bond-stretching potential on two atoms or harmonic
> angle-bending on three (bonded) atoms), you will probably also be better
> off by generating this topology yourself with e.g. a script. In either
> case pdb2gmx probably isn't helpful since it was designed for (bio-)
> polymer-like molecules. I know of someone at Theoretical Chemistry in
> Groningen (Netherlands) who simulated NaCl crystals in Gromacs, although
> I don't remember if he had bonds.
> -- 
> Groetjes,
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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