[gmx-users] Bad energy conservation.
spoel at xray.bmc.uu.se
Wed Dec 4 19:22:21 CET 2002
On Wed, 2002-12-04 at 20:03, Ram'on Garc'ia Fern'andez wrote:
> 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.
rlist is the radius for neighboursearching, however rvdw is the max
distance for vanderwaals calculations and rcoulomb for coulomb.
To get better energy conservation you should set at least
nstlist = 1
constraints = none
Erik L. did quite some testing to obtain better energy conservation,
maybe he can answer.
> 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?
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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