[gmx-users] simmulated annealing excess temperature........................

Elton Carvalho eltonfc at if.usp.br
Mon Aug 20 21:41:59 CEST 2012

On Thu, Aug 16, 2012 at 1:57 PM, tarak karmakar <tarak20489 at gmail.com> wrote:
> Dear All,
> In my simulation I want the temperature of the system to be reached at
> 300 K only after 3 ps. But after 3ps I see temperature became 402 K.
> So am I doing any mistake in the '.mdp' file given below?

> ;temperature coupling is on
> Tcoupl = berendsen
> tau_t = 0.01
> tc_grps = system
> ref_t = 0

Your tau_t seems too short. A value of 0.5 to 1 ps is normally
recommended and used in publications such as [1]. I'm not sure how
realistic such short tau_t is. Also, I'm not sure if a more standard
tau_t would behave with such short allealing cycles. Is tehre any
special reason to use this short cycle istead of an usual velocity
generation (gen_vel)?

[1] Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub,
Luciano T. Costa and David van der Spoel Force Field Benchmark of
Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities,
Surface Tension, Isothermal Compressibility, Volumetric Expansion
Coefficient, and Dielectric Constant, J. Chem. Theor. Comput., 8,
61-74 (2012) doi: 10.1021/ct200731v

Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil

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