[gmx-users] grompp charge group radii larger than rlist

[Thomas Piggot]

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.