[gmx-users] [Fwd: Energy conservation]

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 2 16:30:21 CEST 2006

-------- Original Message --------
Subject: Energy conservation
Date: Wed,  2 Aug 2006 16:40:21 +0300
From: Janne Hirvi <janne.hirvi at joensuu.fi>
To: spoel at xray.bmc.uu.se

Dear David,

I am sorry to disturb you personally outside the gromacs mailing lists but I
would be really pleased if you could help me with energy conservation 
problem I
have struggle for so long time. First of all I would like to thank you for
sending me your parameter file related to your interesting article "The 
of Layer Structure Artifacts in Simulations of Liquid Water". Those 
where pretty equal to mine and I couldn't achieve good energy 
conservation and
would like to know if I am doing something really stupid?

;	File 'mdout.mdp' was generated
;	By user: spoel (291)
;	On host: matisse
;	At date: Sun Aug 11 22:20:40 2002

dt                       = 0.002
nstlist                  = 5
ns-type                  = Grid
pbc                      = xyz
rlist                    = 0.9
coulombtype              = PME
rcoulomb                 = 0.9
vdw-type                 = Cut-off
rvdw                     = 0.9
fourierspacing           = 0.12
pme_order                = 4
ewald_rtol               = 1e-05
tcoupl                   = Berendsen
tau-t                    = 0.1
ref-t                    = 298.15
Pcoupl                   = Berendsen
Pcoupltype               = Isotropic
tau-p                    = 1.0
compressibility          = 5e-5
ref-p                    = 1

If I use previous parameters (without pressure and temperature coupling) to
simulate bulk water with 1372 SPC/E water molecules and with double 
(first equilibriated) I observe drift of approximately +800kJ/mol in the 
energy during 200ps. If I try to remove the effect of van der Waals cut-off
using switch function energy drift increases from before to 
which was quite a surprise. Still enhancing the parameters by decreasing the
value of ewald_rtol to 1E-6 finally decreases energy drift for
+200kJ/mol/200ps. Good energy conservation seems to need even much smaller
value of ewald_rtol and thus larger value of beta.

Cut-off(vdW)(0.9)           1E-5   +793kJ/mol/200ps
Switch(vdW) (0.8/0.85/0.9)  1E-5  +1878kJ/mol/200ps
Switch(vdW) (0.8/0.85/0.9)  1E-6   +236kJ/mol/200ps

Previous values are almost equal or maybe little bit larger than energy 
when using parameters I have employed in my studies 
nstlist=10). Use of van der Waals cut-off always decreases the positive 
drift or changes its sign to negative.

Now I think that I understand much more about energy conservation when using
PME, but I am worried about the my earlier simulations with non energy
conservative parameters and have some questions:

1)First of all I would like to know if you agree with this large energy 
with these parameters or have I done something stupid?

2)If you agree with these values do you see any problems simulating with non
energy conservative parameters when temperature coupling is used?

3)Do you think/agree that when van der Waals cut-off is employed there is no
need to be so demanding about the PME parameters?

I will be very delighted if you have time to comment these issues because I
think you are one of the real experts on this area and I would really need
experts clarification to my own thoughts.



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

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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