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.
Thanks,
Lum
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
