[gmx-users] Re: Inquiry Again.

Erik Lindahl lindahl at stanford.edu
Fri Jul 18 07:13:01 CEST 2003

Hi Victor,

The easy solution is to add a Cu single-atom residue to the .rtp file 
for the forcefield you are using - you can see how it is done for 
several other atoms.

However, be aware that the forcefield included in Gromacs are developed 
for biomolecular simulations - if you have your own set of potential 
parameters (Lennard-Jones?) it would probably be better to use 
optimized ones.

For systems without bonds it is very easy to hack the topology 
manually. Pdb2gmx is primarily useful for molecules with complex bonded 
interactions and residue book-keeping...



On Thursday, July 17, 2003, at 06:33 PM, Victor Kowalenko wrote:

> Hello, GROMACS developers.
> I am interested in running the energy minimization routine mdrun on a
> parallel computer called grendel at the Victorian Partnership for 
> Advanced
> Computing (http://www.vpac.org). Previously I have been using the MMTK
> package to run a python script for a face-centred cubic lattice of
> aluminimum atoms with a layer of copper atoms at its centre. I took a
> pdb file produced by this code and tried pdb2gmx_d to create the 
> topology
> and structure files, but it rejected the copper when creating the
> topology file. I have attached the file to this e-mail, as I am
> wondering what needs to be done so that I can run the mdrun_d program
> on a parallel system.
> Yours faithfully,
> Dr Victor Kowalenko
> Senior Research Fellow
> PS I have attached a sample pdb file previously, but my inquiry gets
> rejected on the grounds that it is too big.
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