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

[Justin A. Lemkul]

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?

In this case, it is safe to ignore the warning.  The DPPC lipids are split 
across the unit cell (which is the problem we're trying to fix, in this case), 
causing the calculated charge group size to be too large.  A charge group that 
claims to encompass over 5 nm is impossible in a system that is approximately a 
6-nm cube, unless the topology is severely broken (which it is not, in this case).

Using -maxwarn 1 is safe here.  Re-running the same grompp on the intact DPPC 
membrane does not raise any error.

-Justin

> 
> Much obliged for your help.
> 
> Cheers,
> Ramon
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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