[gmx-developers] charge group size in grompp

[Jochen Hub]

Hi,

when running grompp for an equilibrated lipid system in a skewed box 
(for having a hexagonal prism), grompp seems to compute the size of of 
the charge groups incorrectly, if the lipids are in a broken representation:

Largest charge group radii for Van der Waals: 9.377, 9.375 nm
Largest charge group radii for Coulomb:       9.377, 9.375 nm
WARNING 1 [file em.mdp]:
   The sum of the two largest charge group radii (18.751873) is larger than
   rlist (1.000000)

When I make the molecules whole by getting first a tpr and then using 
trjconv -pbc mol:

grompp -p topol_pop.top -c pop.pdb -f em.mdp -maxwarn 1
trjconv -s topol.tpr -f pop.pdb -o popw.pdb -pbc mol

grompp is doing ok.
Largest charge group radii for Van der Waals: 0.246, 0.245 nm
Largest charge group radii for Coulomb:       0.246, 0.245 nm

The wrong charge group size is given in all possible until cell 
representations (tric, rect, and compact). When starting

Is that a known issue? I use version 4.5.4-dev-20110321-f8688a9.

Should I submit a bug report?

Thanks,

Jochen

-- 
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Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell&  Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
http://xray.bmc.uu.se/~jochen/index.html
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