[gmx-users] [Fwd: Energy conservation]

[David van der Spoel]

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 
> Origin
> of Layer Structure Artifacts in Simulations of Liquid Water". Those 
> parameters
> 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 
> precision
> (first equilibriated) I observe drift of approximately +800kJ/mol in the 
> total
> 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 
> +1900kJ/mol/200ps,
> 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
> ------------------------------------------------------

Did you use switch or shift? I would definitely recommend the shifted 
potential (for Van der Waals) over a slightly larger range, at least 2 
angstrom

Did you use SETTLE for the constraints?

> 
> Previous values are almost equal or maybe little bit larger than energy 
> drifts
> when using parameters I have employed in my studies 
> (rlist=rcoulomb=rvdw=1.2,
> nstlist=10). Use of van der Waals cut-off always decreases the positive 
> energy
> 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 
> drift
> with these parameters or have I done something stupid?
First off all you did not divide by the number of molecules, so your 
drift really is 0.1 to  0.5 kJ/mol

> 
> 2)If you agree with these values do you see any problems simulating with 
> non
> energy conservative parameters when temperature coupling is used?
Barring other problems, I think that is fine.


> 
> 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?
It depends on the application. For normal simulation with T,P coupling 
the default parameters are fine. For e.g. free energy calculations more 
accuracy may be needed.


> 
> 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.
> 
> Thanks,
> 
> Janne
> 
> ------------------------------------------------------------------------------ 
> 
> 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.
________________________________________________________________________
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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