[gmx-users] grompp output on terminal

Lum Nforbi lumngwegia at gmail.com
Tue Oct 13 17:10:42 CEST 2009

Hello everyone,
   I had written earlier today about my concern involving grompp. I am
trying to minimize the energy of a pure water system using grompp: grompp -f
waters.mdp -c waters_b.gro -p water.top -o watersinput.tpr
and part of the output on the terminal is as follows:

      Analysing residue names:
      Opening library file /usr/local/gromacs/share/gromacs/top
      There are:  2000      OTHER residues
      There are:     0    PROTEIN residues
      There are:     0        DNA residues

      NOTE 1 [file aminoacids.dat, line 1]:
      The optimal PME mesh load for parallel simulations is below 0.5
      and for highly parallel simulations between 0.25 and 0.33,
      for higher performance, increase the cut-off and the PME grid spacing

The problem is I am not specifying any aminoacid file and I am not doing a
parallel run, but the aminoacid.dat file is being opened and the program
assumes that I am doing a parallel run. Is this the way it should be, and
will this affect my run results?
      Please help me out and be patient with me as I am still learning
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