[gmx-users] Hi..

[David van der Spoel]

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.
________________________________________________________________________
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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