[gmx-users] new to gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jun 21 01:35:03 CEST 2007

vijay kumar wrote:
> hi everyone
> I am new to gromacs software all i need to do is
> submit my project in 2 months first thing  i am able
> to do is work with demos ,i did them perfectly but the
> thing is now i need to edit the water molecule pdb
> file and start a new project i.e. now i need to create
> a new pdb file with 20 molecules of water ,generate a
> new topology file and define mdp parameters ,can any
> one please mail me the procedure to start from the
> basics and where  can i find the details of this in
> the Gromacs.org
> the doubts is
> edit a pdb file
> store and retrieve it to command prompt
> define mdp parameters file and use for the program
> and run the simulation
> please send me step by step as given in the demo of
> water molecule

You will find some useful material in the links from this page 
http://wiki.gromacs.org/index.php/Beginners You should also follow 
David's suggestions.


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