[gmx-users] Number of grid cells is zero

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 14 08:53:09 CET 2007

best alep wrote:
> Hi Dr. Dallas,
> Thanks for replying my mail, I've already seen the trajectory file. 
> There's no structure.. I saw only dots.. these dots were not connected 
> with each other. But the colors shows the difference of the atoms 
> (probably). What is happening? Can you or anyone help me please? I'm new 
> to this (molecular simulation)..so my basic is not strong. Is it 
> concerning my simulation box? or my mdp file?..By the way, I'm trying to 
> run simulation on Oleyl oleate C36 O2 structure.
> Clues, or comments or advices please...
your starting structure is bad. fix it with minimization etc.

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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