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

[Mark Abraham]

Hi,

That's entirely normal for condensed-phase systems. Negative PE means the
system doesn't want to fly apart. Conventionally, zero PE is when every
particle is infinitely separated - look at the form of the expression for
energy in electrostatics (and gravity)

Mark

On Wed, 18 Mar 2020 at 06:28, Anh Vo <atv55 at msstate.edu> wrote:

> 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
> --
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