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
information.
Basically, all the output is entirely normal. As long as grompp isn't spitting
out warnings/errors, you should be fine to continue.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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