[gmx-users] Error with grompp for EM

[Erik Lindahl]

Valentin Gogonea wrote:

> Dear Gromacs users:
>
> I am trying to do simple energy minimization with gromacs for small 
> molecules (e.g. amino acids). I don't want to use cut-off. I looked in 
> the manual and I set up the parameters as bellow:
>
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  100
> nstlist             =  0
> ns_type             =  grid
> rlist               =  0.0
> rcoulomb            =  0.0
> rvdw                =  0.0
> coulombtype         =  cut-off
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000.0
> emstep              =  0.01
>
> I get the following error in output.grompp_em:
>
> ERROR: can only have neighborlist cut-off zero (=infinite)
> with coulombtype = Cut-off or coulombtype = Userand simple neighborsearch
> without periodic boundary conditions (pbc = no) and
> rcoulomb and rvdw set to zero
> Excluding 3 bonded neighbours for Protein_A           1
> processing coordinates...
> double-checking input for internal consistency...
> Fatal error: There was 1 error
>
> I am probably doing something wrong, but I don't know what. I would 
> appreciate any help.
>
> Thank you.
>
> Valentin


Hi,

Since you don't use cutoffs at all it isn't possible to use periodic 
boundary conditions (that would mean an infinite amount of interactions. 
Without the periodic boundary conditions it isn't possible to use grid 
neighborsearching which is based on the periodic box.

So, just swith to simple neighborsearching as it says after the error!

Cheers,

Erik