[gmx-users] gromacs 4.0 vs 4.5

[Amit Choubey]

Hi all,

I am doing dppc-water simulation. I am using structure and topologies from

http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies

In version 4.0 when i do
grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top

it creates npt.tpr without any errors.

Using the same structure and topologies when i issue

grompp_v4.5.3 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top

it gives out the following warning

Largest charge group radii for Van der Waals: 5.354, 5.297 nm
Largest charge group radii for Coulomb:       5.354, 5.297 nm
WARNING 1 [file npt.mdp]:
  The sum of the two largest charge group radii (10.650990) is larger than
  rlist (1.200000)

I dont think the charge group should be so big. Can someone suggest what is
going on ?

Ami
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