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
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