[gmx-users] Energy conservation of rigid water models

Janne Hirvi janne.hirvi at joensuu.fi
Thu Feb 16 18:17:17 CET 2006


I have read several messages about energy conservation problems and solutions
but however I am not sure if I have done something stupid. I have used time
step of 2.0fs for rigid SPC and SPC/E water models in simulations of bulk water
(NPT) and water droplets on frozen polymer surfaces (NVT). Everything seemed to
be just fine but when I tested energy conservation of bulk model in NVE
ensemble I was terrified.

NVE bulk simulation of 1372 rigid SPC water molecules with 2fs time step (total
time 500ps) resulted in huge drift in total energy. I used same parameters as
for other simulations and even those aren't optimal I expected atleast
something better. Energy conservation seemed to be adequate only when I used as
short time step as 0.5fs.

Time step (fs)      Total Energy (kJ/mol)      Drift   

2.0                 -45596.6                   1235.5
1.0                 -46147.5                   330.974
0.5                 -46331.1                   <10 (not yet finished)


comm-mode                = None or Linear
nstlist                  = 5 or 10
rlist                    = 1.2
coulombtype              = PME
rcoulomb                 = 1.2
vdw-type                 = Cut-off
rvdw                     = 1.2
fourierspacing           = 0.12
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
tcoupl                   = No
Pcoupl                   = No

Bad energy conservation indicates that employed time step of 2.0fs is too long
but however other results from NPT bulk simulations are reasonable. Moreover I
think that its quite normal to use this long time step for rigid water
molecules. So I am willing to know if this large energy conservation problems
are acceptable and are they atleast "partially compensated" in NPT or NVT
ensemble when temperature coupling prevents heating of the system?

Thanks for any help or comments! 


Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi

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