[gmx-users] Error running 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. 




What is the best approach here to correct this? 

Thanks! 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]