[gmx-users] Re: Inquiry Again.

Victor Kowalenko victork at mail.csse.monash.edu.au
Fri Jul 25 09:31:01 CEST 2003

Hi Anton,

I am sending you this e-mail to confirm that the following is all
I need to get our atomic modelling working in GROMACS as I am not entirely
sure that this will work.

First, I need to write a script file that will create *.top file from the
pdb files. I should mention the format of our pdb files just in case their
format is unsuitable for GROMACS. They basically go like this:

HETATM  <Particle No.> <Type> <Type> <Particle No.> x y z 0.00 0.00 <Type>
HETATM     1             Al     Al      1           0 0 0 0.00 0.00  Al
HETATM     2             Cu     Cu      2           0 0 1 0.00 0.00  Cu

I think the zeros correspond to velocities or some other units, but they
are irrelevant for the time being. It is x, y and z coordinates that are 
important. I would like to know if this format is suitable for GROMACS or
whether I need to write a script file that extracts only the coordinates.
The files will have to be altered anyway as the coordinate positions are
in Angstroms while there is a preference for nm in GROMACS.

As far as the topology file is concerned, it appears to me that if I elect 
only to do atom interactions I only need to create a script file that
creates a topology file with only 2 main parts to it: [atomtypes] and
[atoms]. That is, it should look like:

; specify the various types of atoms in the simulation
; atom atomic mass charge epsilon                sigma
  Al     26.98      0      LJ_energy in kJ/mol   LJ_radius in nm
  Cu     63         0      LJ_energy_2 in kJ/mol    LJ_radius_2 in nm
; nr  atom type
  1      Al
  2      Cu
  3      Al

where the numbers in the [atoms] correspond to the numbers in the pdb
files so that GROMACS can get the particle coordinates. 

I think this is what you are saying below and if this is correct, then
I see no problem in writing a little script file to read the pdb file
a structure file. Please inform me as to whether this is correct or
whether I have missed something. My aim is to create a general script
file that will variable numbers of particles in the pdb files and place
them in this format. If the pdb format is no good, then I could create a
new pdb file with the proper format. 


On Wed, 23 Jul 2003, Anton Feenstra wrote:

> 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)
> -- 
> Groetjes,
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| 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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