[gmx-users] new to gromacs

David van der Spoel spoel at xray.bmc.uu.se
Wed Jun 20 21:56:58 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 want to read chap 5 of the manual
you can do all this with a text editor.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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