[gmx-users] grompp output on terminal

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 13 22:05:40 CEST 2009

Lum Nforbi wrote:
> 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/aminoacids.dat
>       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 
> gromacs.

The aminoacids.dat is a generic input file that tells grompp what is protein and 
what is not.  In your case, it simply doesn't matter.

The note about PME is also standard output, since parallel runs are quite 
common, this is useful information.  There is no way for grompp to know if you 
are going to be running in parallel, but it's simply providing you useful 

Basically, all the output is entirely normal.  As long as grompp isn't spitting 
out warnings/errors, you should be fine to continue.


> Thanks,
> Lum
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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