[gmx-users] energy decreasing in NVE simulation

Yun-an Yan yun-an.yan at uni-rostock.de
Wed May 19 17:59:23 CEST 2010

Dear all,

When I try to simulation with NVE ensemble, the
total energy keeps decreasing. Geometry optimization
and solvent equilibration are done before the NVE simulation.

I follow the requirements provided in

Would any one help me to figure out what was wrong with
my settings?

Millions of thanks and best wishes,

BTW: Please check the following for the .mdp file

;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator               = md
;time step in femtoseconds
dt                       = 0.001
;number of steps
nsteps                   = 10000000
;No constraints
constraints              = none
constraint_algorithm     = shake
shake_tol                = 1e-08

; group(s) for center of mass motion removal
comm-grps                = AA CCl4
; frequency for center of mass motion removal
nstcomm                  =  1000
;frequency to write coordinates to output trajectory file
nstxout                  = 1000
;frequency to write velocities to output trajectory file
nstvout                  = 1000
;frequency to write energies to log file
nstlog                   = 1000
;frequency to write energies to energy file
nstenergy                = 1000
;group(s) to write to energy file
energygrps               = System

;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist          = 10
ns_type          = grid
rlist            = 1.5

; Use periodic boundary conditions in all directions.
pbc = xyz

;cut-off distance for the short-range neighbor list
;treatment of electrostatic interactions
coulombtype      = PME-switch
fourierspacing   = 0.12
pme_order        = 4
ewald_rtol       = 1e-5
rcoulomb_switch  = 1.0
rcoulomb         = 1.2

;treatment of van der waals interactions
vdwtype          = Switch
rvdw-switch      = 1.0
rvdw             = 1.2
dispcorr         = EnerPres

;Temperature coupling
tcoupl          = no

;Pressure coupling
pcoupl           = no

;Velocity generation
gen_vel          = no

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