[gmx-users] gromacs 4.0 vs 4.5

[Justin A. Lemkul]

Amit Choubey wrote:
> 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 ?
> 

The input file contains broken molecules.  There is nothing wrong, per se, but 
only in the case when molecules are split across periodic boundaries.  This is a 
new check as of version 4.5.

-Justin

> Ami
> 

-- 
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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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