[gmx-users] 2 beginner´s questions

[paloureiro at biof.ufrj.br]

Quoting joao at lnls.br:

> 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?
You can use VMD, also.

>
> 2. This is the near the end of my .top file in the final MD step:
>
> #ifdef POSRES_WATER
> ; 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?
No, just do NOT write -DPOSRES_WATER in the "define = " line in your  
[].mdp file.

Regards,

Pedro.

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