[gmx-users] Hi..

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 16 10:07:23 CEST 2006

Navratna Vajpai wrote:
> Hey Mark..
> I had attached the file along with the mail. I think you could 
> not receive it. let me paste the contents and explain it little more. 
> I am trying to run the simulation in vacuum of a nona peptide. I managed 
> to get pdb2gmx working and even further the EM working. But when I tried 
> to do the MD run after a small minimization of protein, I got an error 
> message after the execution of grompp. The execution asked for the -n 
> option which indicates for the index file. 1) I don't know why it asked for?
> 2) If it ask for is there any way to solv this problem. Actually i tried 
> using that also. But the error stayed back. 
> I am also pasting the error after the grompp. Somehow this could not 
> prepare the input file for the MD run. 
> 3) third question is: I am wondering whether i can start my run just 
> after the execution of pdb2gmx. Any ways 1) the system is in vacuum and 
> second while running it for quite long, minimization of energy will 
> automatically take place.
You should probably start by doing the tutorial and browsing the web 
site, check out the flow chart for doing simulations.
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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