[gmx-users] Re: learning gromacs question

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 16 00:40:36 CEST 2007

David van der Spoel wrote:
> On Wed, 15 Aug 2007, burkhard rammner wrote:
>> Dear David,
>> although I am a former biochemist (and do now 3D productions for 
>> scientific purposes) I never came in contact with MD before.
>> Besides my "normal" molecule visualisation stuff I now try to do protein 
>> folding with gromacs.
>> What I do is:
>> create a protein myself, fold it to a some degree manually.

Why not use a folded structure from the PDB? De novo folding of proteins 
lacking structural homology is an unsolved problem.

>> Then I would need to do short MD to let the protein zip together, to get 
>> a "scientiffically correct" folded protein.
>> So, all I want to do is a hopefully simple energy minimisation and MD.
>> Now my question to you is:
>> Does it make sense to try to learn Gromacs myself, or would I have to 
>> definitely take some semesters at the university?

It would be extremely rare for a university to have courses worth doing 
for this limited objective.

>> Are there resources, other than the manual and some internet tutorials 
>> which could aid me?

No. You'll need to do some work reading the manual and the tutorials and 
probably do your own background reading elsewhere too. The GROMACS 
manual has a reasonably good introduction to doing molecular simulation. 
http://wiki.gromacs.org also has some useful material.



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