[gmx-users] Energy values for 1 step NVT/NVE simulation of 100 water molecules

[Anh Vo]

Hi everyone,

I am doing just a small simulation of 100 water molecules (after energy
minimization, I run only 1 step of NVT and then get the Total energy,
Potential and Kinetic energy from .edr file). The Kinetic energy is around
1 kJ/mol, while the Potential and Total energy is below - 2000 kJ/mol
(around - 2405 kJ/mol). Similar results are obtained at 310K and 1K, as
well as when I run NVE instead of NVT. Is it possible for the energy to be
that much negative? If not, what could I have missed?
Please see my settings in .mdp file as below for the 1 step NVT (For NVE,
similar settings are used, but with tcoupl = no and  pcoupl  = no).

define              = -DREST_ON -DSTEP6_1
integrator         = md
dt                     = 0.0005
nsteps             = 1
nstlog              = 1
nstxout            = 1
nstvout            = 1
nstfout             = 1
nstcalcenergy  = 1
nstenergy        = 1
;
cutoff-scheme   = Verlet
nstlist                = 10
rlist                   = 1.0
coulombtype    = pme
rcoulomb          = 1.0
vdwtype            = Cut-off
vdw-modifier     = Force-switch
rvdw_switch      = 0.8
rvdw                  = 1.0
;
tcoupl                = berendsen
tc_grps              = SOL_ION
tau_t                  = 1.0
ref_t                   = 310
;
pcoupl   = no
;
constraints         = h-bonds
constraint_algorithm    = LINCS
;
nstcomm            = 100
comm_mode      = linear
comm_grps        = SOL_ION
;
refcoord_scaling        = com


Thank you very much for your help. I really appreciate it.

Best,
Anh Vo