[gmx-users] potential energy

Meenakshi Rajput ashi.rajput39 at gmail.com
Mon Aug 11 11:02:35 CEST 2014

hi users
i have run energy minimisation of docked complex by using this min.mdp:-

cpp        = /lib/cpp    ; Preprocessor
include        = -I../top    ; Directories to include in the topology
integrator    = steep
emtol        = 1000        ; Stop minimization when the energy changes by
less than emtol kJ/mol.
nsteps        = 200        ; Maximum number of (minimization) steps to
nstenergy    = 10        ; Write energies to disk every nstenergy steps
nstxtcout    = 10        ; Write coordinates to disk every nstxtcout steps
xtc_grps    = Protein    ; Which coordinate group(s) to write to disk
energygrps    = Protein    ; Which energy group(s) to write to disk
nstlist        = 5        ; Frequency to update the neighbor list and long
range forces
ns_type        = grid      ; Method to determine neighbor list (simple,
rlist        = 1.2        ; Cut-off for making neighbor list (short range
coulombtype    = PME       ; Treatment of long range electrostatic
rcoulomb    = 1.2        ; long range electrostatic cut-off
rvdw        = 1.2        ; long range Van der Waals cut-off
constraints    = none        ; Bond types to replace by constraints
pbc        = xyz        ; Periodic Boundary Conditions (yes/no0
After the run, potential energy is negative. can you tell me whats the

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