[gmx-users] Hi..

Erik Marklund erikm at xray.bmc.uu.se
Wed Aug 16 11:34:16 CEST 2006

On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote:
> 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?

My guess it's because of this line in the mdp file:
tc-grps     =  protein      sol

Apparently you have temperature-coupled the solvent, even though you
have no solvent. Vacuum, right? Note that grompp is looking for 'sol'
and, when it can't find it among the default groups (see manual), it
looks for an index file:

Fatal error:
Group sol not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.
In that case use the '-n' option.

Try removing 'sol' from the mdp file. If you are simulating in vacuum,
you (probably) have no solvent.


> > 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.
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se

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