[gmx-users] doubt in grompp.mdp(output control options)

[leafyoung81-group at yahoo.com]

--- Rahul Karyappa <r.karyappa at ncl.res.in> wrote:

> 
> Dear all,
> 
>      My system consists of a polymer chain
> surrounded by water molecules and ions. In the
> grompp.mdp file (in the
> OUTPUT CONTROL OPTIONS), I am specifying xtc-grps
> and energygrps as
> only protein. Is this correct or I need to specify
> SOL also????

Four question marks are very annoying. I suggest you
to read
Eric S. Raymond's How To Ask Questions The Smart Way
http://www.catb.org/~esr/faqs/smart-questions.html
> 
> 
> ; OUTPUT CONTROL OPTIONS
> 
> ; Output frequency for coords (x), velocities (v)
> and forces (f)
> 
> nstxout                  = 0
> 
> nstvout                  = 0
> 
> nstfout                  = 0
> ow 
> ; Checkpointing helps you continue after crashes
> 
> nstcheckpoint            = 1000
> 
> ; Output frequency for energies to log file and
> energy file
> 
> nstlog                   = 500
> 
> nstenergy                = 500
> 
> ; Output frequency and precision for xtc file
> 
> nstxtcout                = 500
> 
> xtc-precision            = 1000
> 
> ; This selects the subset of atoms for the xtc file.
> You can
> 
> ; select multiple groups. By default all atoms will
> be written.
> 
> xtc-grps                 = Protein
If you would like to analyse the movement of
solvents/ions, you can add SOL here.
> 
> ; Selection of energy groups
> 
> energygrps               = Protein
Similarly, but for energy observation. 

These two options do not affect MD.
> 
> 
> looking forward to your kind reply.
> 
> 
> Rahul Karyappa
> 
> NCL, Pune
> 
> 
> 
> 
> 
> 
>
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