[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
format
integrator = steep
emtol = 1000 ; Stop minimization when the energy changes by
less than emtol kJ/mol.
nsteps = 200 ; Maximum number of (minimization) steps to
perform
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,
grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range
forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
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
problem??
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