[gmx-users] Re: Inquiry Again.

[Victor Kowalenko]

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.