[gmx-users] Error running mdrun em with Sodium ions in GMX 5.14

[Sergio Manzetti]

Hi, I have a system with DNA and water, and given the charge of the DNA of -20, genion was used to add +20 charge to the gro file. The energy minimization step gives then a warning: 

WARNING 2 [file em.mdp]: 
The sum of the two largest charge group radii (16.704304) is larger than 
rlist (1.200000) 



Which is the ignored using maxwarn option. 

When getting to the em step: 

Fatal error: 

step 25: Water molecule starting at atom 31535 can not be settled. 
Check for bad contacts and/or reduce the timestep if appropriate. 


However, these are not waters, but there are sodium ions added to the system by replacing 20 water molecules, which grompp thinks are waters. The index file does not contain info about these, as also there, the Sodium are not identified and differentiated from water molecules. 


What is the best approach here to correct this? 

Thanks! 

Sergio Manzetti 

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