[gmx-users] Issues with energy when running in the microcanonical ensemble

[C.M.Sampson]

Dear all,

I'm using Gromacs 4.5.5 with the amber ff99SB forcefield to run NVE
simulations on ethane in 725 TIP3P water molecules.  I used antechamber
to parametrise my ethane.

I have 2 issues;

Firstly the energy conservation of my simulations seems to get worse as
I lower my timestep, here is an example .mdp file that I'm using:


integrator      = md-vv
gen_vel         = no
nsteps          = 1000000
dt              = 0.001
nstlist         = 10
rlist           = 1.3
coulombtype     = pme
rcoulomb        = 1.0
vdw-type        = Shift
rvdw            = 1.0
tcoupl          = no
pcoupl          = no
nstenergy       = 100

I found a link describing that it could be an issue with the precision
and that Gromacs can be installed with double precision:

http://www.gromacs.org/Documentation/Terminology/Conserving_Energy

but is this the only way to ensure energy conservation?

My second issue is with the calculation of the kinetic energy, I have
2183 atoms in my simulation box which means the kinetic energy should be
(roughly)

0.5 * 3*2183-3(degrees of freedom) * 0.001987204118(kB) * 300(T) *
4.184(conversion from kcal/mol to kJ/mol) = 8163.97

however, when I look in my simulation the kinetic energy Gromacs outputs
is 5498.20 

           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
       Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
5.95743e+00    1.96046e+01    4.71247e-01    5.73520e-01    3.92661e+00
    LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
5.12842e+03   -3.20604e+04   -2.67111e+03   -2.95726e+04    5.49820e+03
    Total Energy    Temperature Pressure (bar)
   -2.40744e+04    3.02575e+02   -1.82251e+03

By running in NVE I'm not using a thermostat and can't find any reason
in the manual to scale the kinetic energy.  Is there an a reason I'm
missing as to why my kinetic energy seems lower than it should be?

Best Wishes

Chris