[gmx-users] mdp file

David spoel at xray.bmc.uu.se
Fri Jun 27 15:58:01 CEST 2003

On Fri, 2003-06-27 at 14:18, Derrick Guang Yuh Lee wrote:
> i am recently new to Gromacs and since there is no local expert on this
> program where i am, i am posting here for help.
> i am currently working on a pdb file for a DPPC lipid bilayer. now, i want
> to view the program in the Gromacs GUI (after its done with mdrun, etc).
> so i need specific files to do all of that stuff, which include a top,
> gro, and the pdb file (please corret me if there are extra files needed
> besides these and the stand library), as well as an mdp file. my question
> is though, the mdp file can be created by myself, but if so, how do i know
> it is set up correctly?
Basically the online manual tells you what the options mean. Furthermore
it may be good to read some recent literature on membrane simulations
(e.g. from Erik Lindahl,  Peter Tieleman, or SJ Marrink) and check their
methods section. In particular the treatment of Coulomb interactions.

>  - derrick
>  derrick Lee
>  faculty of Science
>  Memorial University of Newfoundland
>  k24dgyl at mun.ca or derrickglee at hotmail.com
> "a teacher is never a giver of truth - he is a guide, a pointer to the
> truth that each student must find for himself. a good teacher is merely a
> catalyst." 
>                                                               - bruce lee
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel

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