Quoting [EMAIL PROTECTED]:
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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