[gmx-users] Problem in setting rlist, rcoulomb

[Mark Abraham]

nur avneet wrote:

> for my run...the terminal gives an error as:
> "the cut off length is longer then half the shortest box vector or 
> longer then the smallest box diagonal element. Increase the box size or 
> decrease the rlist."

Actually this error message is from grompp and it means what it says. 
The structure file you have provided implies a box size - if a .gro 
file, then the last line contains box vectors. These have the 
constraints implied by the error message. Use editconf and/or genbox to 
fix whatever is wrong.

> What does this error mean..as i have not added any box yet.
> 
> then  i change the rlist to 0.3, & rcoulomb & rvdw to 0.2 and 
> rcoulomb_switch & rvdw_switch to 0.1 . The error gets removed..but for 
> trying other values for these parametrs in between these and the initial 
> values given in the mdp file above, the error reappears.

This is not the way to do a sensible MD calculation. If you don't know 
why that is, I suggest reading the first chapters of the manual, paying 
particular attention to description of the non-bonded and electrostatic 
interactions.

Mark