Option     Filename  Type         Description
------------------------------------------------------------
  -f         md.mdp  Input        grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c nvtWprotonated.gro  Input        Structure file: gro g96 pdb tpr etc.
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n      index.ndx  Input, Opt!  Index file
  -p      topol.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o MD_B2ar_XW_protonated_100ns.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-[no]v       bool   no      Be loud and noisy
-time        real   -1      Take frame at or first after this time.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
                            sites
-maxwarn     int    0       Number of allowed warnings during input
                            processing. Not for normal use and may generate
                            unstable systems
-[no]zero    bool   no      Set parameters for bonded interactions without
                            defaults to zero instead of generating an error
-[no]renum   bool   yes     Renumber atomtypes and minimize number of
                            atomtypes

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

NOTE 1 [file md.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy

Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'XW'
Excluding 3 bonded neighbours molecule type 'CCl4'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
Excluding 1 bonded neighbours molecule type 'CL'
Number of degrees of freedom in T-Coupling group Protein_XW_CCl4 is 17340.00
Number of degrees of freedom in T-Coupling group SOL_NA_CL is 59121.00
Estimate for the relative computational load of the PME mesh part: 0.38

NOTE 2 [file md.mdp]:
  This run will generate roughly 26245 Mb of data


There were 2 notes

Back Off! I just backed up MD_B2ar_XW_protonated_100ns.tpr to ./#MD_B2ar_XW_protonated_100ns.tpr.2#

gcq#37: "They Were So Quiet About It" (Pixies)

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mpiexec was unable to launch the specified application as it could not find an executable:

Executable: -p
Node: ib03

while attempting to start process rank 0.
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