[gmx-users] Water molecule can not be settled - mdrun error

[Lara Bunte]

Hello

My equilibration of water around lumiflavin works (I got no error, no warning and no note). Sadly the mdrun fails with following error:

step 886: Water molecule starting at atom 7596 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

What does GROMACS mean with "check bad contacts" and what do you think I should fix? 


System is lumiflavin in water, CHARMM 27 force field, tip3p water model. 

Here is my mdp file I used before:

define          = -DPOSRES

integrator      = md
dt              = 0.002
emtol           = 1000.0        
emstep          = 0.01          
nsteps          = 5000          

nstlist         = 1             
rlist           = 1.2            
rlistlong       = 1.4           
rcoulomb        = 1.2           
coulombtype     = pme
vdw-type        = cut-off
rvdw            = 1.2           

nstxout         = 100           
nstvout         = 100           
nstenergy       = 100           
nstlog          = 100           

tcoupl          = V-rescale     
tc-grps         = ISO SOL       
tau_t           = 0.1   0.1     
ref_t           = 300   300     

pcoupl          = no


Thanks for helping me

Greetings
Lara