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: [EMAIL PROTECTED] & [EMAIL PROTECTED]
------------------------------------------------------------------------------
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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