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

Rahul Karyappa r.karyappa at ncl.res.in
Fri Sep 16 08:02:56 CEST 2005

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????


; Output frequency for coords (x), velocities (v) and forces (f)

nstxout                  = 0

nstvout                  = 0

nstfout                  = 0

; 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

; Selection of energy groups

energygrps               = Protein

looking forward to your kind reply.

Rahul Karyappa

NCL, Pune

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