[gmx-users] Problem in setting rlist, rcoulomb
Mark.Abraham at anu.edu.au
Fri Nov 10 10:48:53 CET 2006
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
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