[gmx-users] Bad energy conservation.

[Ram'on Garc'ia Fern'andez]

I am having problems with energy not being conserved with Gromacs. I tried
reducing the timestep with no sucess.

My simulation box contains 432 diatomic molecules. In reduced units, bond
length is 1 and temperature is 2. My reduced time is about 10^(-4), so
it is a very small timestep. There should be no overlaps, since the original
structure is a crystal (and the initial energy is negative).

I tried the example simulation of water included in the tutor directory
I removed both the termostat and the barostat, and changed both the
vdw type and coulombic type to shifted. Gromacs manual says than with
the potential type is shifted, rlist should be higher than rvdw and rcoulombic,
but grompp emits an error if rlist is higher than rvdw or rcoulombic. Anyway,
I am not sure if I understand exactly what is rlist.

The energy is not at all conserved in this simulation. Values of total energy are:

step  Total energy
0     -7.48040e+03
50    -7.44887e+03
100   -7.41691e+03
150   -7.39175e+03
200   -7.36756e+03
250   -7.34220e+03
300   -7.30953e+03
[...]
5000  -3.78888e+03

Energy is not quite correct.

Could anyone show any simulation with Gromacs where energy is conserved?

Ramon