I think this is because (if I remember correctly) in the downloaded DPPC
bilayer from Peter Tieleman's website the lipids have not been made
whole again and so are split across the periodic boundaries. If you run
a minimisation (so set -maxwarn to 1 during grompp) and re-run grompp on
the minimised structure you should see that this "problem" disappears.
Cheers
Tom
Dr. Ramón Garduño-Juárez wrote:
Dear All:
I am going through the Justin Lemku tutorial for KALP15 in DPPC. I have
reached step three, when I try to generate a trp file for DPPC only by
means of :
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
I get the following warning:
WARNING 1 [file minim.mdp]:
The sum of the two largest charge group radii (10.651017) is larger than
rlist (1.200000)
which causes grompp to be terminated.
Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
I do not know if I should ignore this warning and use -maxwarn, or if I
must modify the mdp file.
By the way, I have assigned values from 1.0 to 1.4 to rlist, rcoulomb
and rvdw, but I get the same warning all the time...
Any idea as to what causes this problem?
Much obliged for your help.
Cheers,
Ramon
--
Dr Thomas Piggot
University of Southampton, UK.
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