[gmx-users] 2 beginner´s questions

Alan Dodd anoddlad at yahoo.com
Mon May 15 17:56:19 CEST 2006

--- joao at lnls.br wrote:

> Dear Gromacs community.
> I am just starting my first dynamics and wonder if
> you could help me with:
> 1. Want to use some graphical program to see the
> atoms moving. Can I use 
> ngmx? What other programs are available?

Yes, ngmx will work just fine, albeit crudely.  VMD is
another good option - has reasonably good graphics and
analysis features, and lets you convert a trajectory
into a movie.  There are other trajectory viewing
programs out there, but I don't think they can read
GROMACS trajectories.

> 2. This is the near the end of my .top file in the
> final MD step:
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
> If I want the waters to be free, should I comment
> out these lines?

I'm pretty sure position restraints only turn on if
you specify them to in your .mdp file.  You'll notice
the first line of your statement contains the word IF.
 The default is for no PR.  Look at the mdp files in
the share/tutorial/ folders.

> Thank you, João.
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