[gmx-users] Re: Inquiry Again.
victork at mail.csse.monash.edu.au
Fri Jul 18 09:46:01 CEST 2003
Thank you for the information. I really was very sloppy about the
force-field and when I did apply pdb2gmx to my pdb file, I specified a
force-field of 0, not realising how critical this was. I realise now that
I should perhaps tried 1 instead of 0. I will look into this more on
Monday after delving into the relevant sections of the manual.
Yes we are using a Lennard-Jones potential and when I run the code in MMTK
we need to specify the parameters. I guess I can use these parameters
except that I do not know enough about GROMACS to do so. I guess I have
to look at .rtp files in more detail.
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.
In any case, thank you for your response.
On Thu, 17 Jul 2003, Erik Lindahl wrote:
> 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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