[gmx-users] Error with grompp for EM

Valentin Gogonea v.gogonea at csuohio.edu
Thu Mar 28 02:00:20 CET 2002

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.


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