[DFTB-Plus-User] A MD process including three molecules has failed

[Ben Hourahine]

Dear Zhang,

did you pre-optimise your geometry to a good minimum before starting the
MD? What you are describing (but please include the geometry to specify
the full code input), sounds like a common three body collision effect.
What are the energy components (kinetic and Mermin energy) at the start
of the calculation and after dissociation? Also remember that your
boundary conditions are for the three molecules in vacuum - is a bound
system at 200 K?

Regards

Ben

On 22/05/15 08:15, 张海杰 wrote:
> Dear All:
>
> We have done a MD process including a sulfuric acids and two ammonia
> with the DFTB.
> These three molecules contact with each other through hydrogen
> bonds. The time scale of 
> MD is 100ps. The result shows that after 50ps only
> one  ammonia contact with sulfuric acids
> through hydrogen bonds. The another ammonia has gone further away from
> the sulfuric making
> the distance several tens angstrom or even more.I attached the
> dftb_in.hsd to search help.I
> would be really thankful for any help.
>
> Best regards.
> Haijie Zhang
>
> Geometry = GenFormat { <<< "geom-opt.gen" } Driver = VelocityVerlet {
> Steps = 100000 TimeStep [Femtosecond] = 1.000000000000000 Thermostat =
> NoseHoover { Temperature [Kelvin] = 200 CouplingStrength [cm^-1] = 800
> } OutputPrefix = "geom.out" } Hamiltonian = DFTB { SCC = Yes
> SCCTolerance = 1.0E-005 # Identical to Fan MaxSCCIterations = 9999
> Mixer = Broyden { MixingParameter = 5.000000000000000E-002
> CachedIterations = 8 } MaxAngularMomentum = { O = "p" H = "s" N = "p"
> S = "p" } Charge = 0.000000000000000E+000 SpinPolarisation = {}
> Eigensolver = Standard {} # Slow! Dispersion = LennardJones {
> Parameters = UFFParameters {} } Filling = Fermi { Temperature [Kelvin]
> = 1.000000000000000E-008 } SlaterKosterFiles = { O-O =
> "/home/lt/3ob-2-1/O-O.skf" O-H = "/home/lt/3ob-2-1/O-H.skf" O-N =
> "/home/lt/3ob-2-1/O-N.skf" O-S = "/home/lt/3ob-2-1/O-S.skf" H-O =
> "/home/lt/3ob-2-1/O-H.skf" H-H = "/home/lt/3ob-2-1/H-H.skf" H-N =
> "/home/lt/3ob-2-1/N-H.skf" H-S = "/home/lt/3ob-2-1/S-H.skf" N-O =
> "/home/lt/3ob-2-1/N-O.skf" N-H = "/home/lt/3ob-2-1/N-H.skf" N-N =
> "/home/lt/3ob-2-1/N-N.skf" N-S = "/home/lt/3ob-2-1/N-S.skf" S-O =
> "/home/lt/3ob-2-1/S-O.skf" S-H = "/home/lt/3ob-2-1/S-H.skf" S-N =
> "/home/lt/3ob-2-1/S-N.skf" S-S = "/home/lt/3ob-2-1/S-S.skf" }
> ReadInitialCharges = No } Options = { WriteAutotestTag = Yes
> RandomSeed = 12321 } ParserOptions = { ParserVersion = 4 }
>
>
>
>
>
>
>
>
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user

-- 
      Dr. B. Hourahine, SUPA, Department of Physics,
    University of Strathclyde, John Anderson Building,
            107 Rottenrow, Glasgow G4 0NG, UK.
    +44 141 548 2325, benjamin.hourahine at strath.ac.uk

2013/4 THE Awards Entrepreneurial University of the Year
      2012/13 THE Awards UK University of the Year

   The University of Strathclyde is a charitable body,
        registered in Scotland, number SC015263

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20150522/4be0aaed/attachment-0001.html>