[gmx-users] Go-model Hamiltonian

[Xavier Periole]

On Tue, 15 Jan 2008 08:20:05 -0600
  eddie mendel <pckboy at gmail.com> wrote:
> Greetings Gromax users!
> 
> 
> 
> I am trying to do free energy calculations using a Go-model Hamiltonian 
>simulation, and I was wondering if GROMACS has such capabilities.
> 
> I was planning to use CHARMM but I found a problem at a server that builds 
>the respective  Go-model Hamiltonian from a pdb  file

I do not know anybody who as used a Go-model in GMX but it should not be
so difficult using tabulated potentials!

> this is the website in case you are interested: 
>http://mmtsb.scripps.edu/webservices/gomodel.html

What is wrong with the website server? Does it give a wrong "topology"?
We have been using it for a peptide and that would be nice if you could
detail the "bug".

> Please let me know any suggestions you may have. My protein has around 500 
> residues and hence I think a Go-model is the only viable
> option I have.

Depends on what you are after. We have developed a Coarse Grain model
for proteins and it can handle enormous systems without problems. It
should be out in a few months.

XAvier
> 
> Thanks for the advice beforehand
> 
> 
> 
> Eduardo Mendez
> PhD Candidate and so forth
> Department of Biochemistry
> University of Saskatchewan,
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------