*Dear all,
I am trying to minimize the energy of the single molecule
using gromacs. I tried with the following mdp
; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE
include =
define =
; RUN CONTROL PARAMETERS
integrator = steep
nsteps = 5000
init_step =
; ENERGY MINIMIZATION OPTIONS
emtol = 10
emstep = 0.01
nstcgsteep =
nbfgscorr =
nstcheckpoint = 100
nstlog = 100
nstenergy = 1
; SIMULATED ANNEALING
annealing = no
annealing_npoints =
annealing_time =
annealing_temp =
But it shows the following error,
ERROR: The cut-off length
is longer than half the shortest box vector or
longer than the smallest box diagonal element. Increase the box size or
decrease rlist.
I have not included any the cut-off in the mdp file, but it still shows
the error. Am I supposed to include something to mdp to run single molecule
energy minimisation.
Thank you*
*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.
+91-9686933963.*
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