[gmx-users] Question about annealing and thermostat
David
spoel at xray.bmc.uu.se
Wed Aug 31 20:22:47 CEST 2005
On Wed, 2005-08-31 at 13:46 -0400, Leonardo Sepulveda DurĂ¡n wrote:
> hello!!
>
> I am making high temperature simulations (500 K) and to avoid abrupt
> disruption of structure I use
>
> Tcoupl = berendsen
> tau_t = 0.1 0.1
> tc-grps = Protein SOL
> ref_t = 498 498
>
> Pcoupl = berendsen
> tau_p = 0.5
> compressibility = 4.5e-5 ; compresibilidad del H2O a
> 300K y 1 atm (en bar-1);
> ref_p = 1.0
>
> annealing = single single
> annealing_npoints = 2 2
> annealing_time = 0 50 0 50
> annealing_temp = 1 500 1 500
>
> the last annealing command make a linear increase of temperature from
> 1 to 500 K in 50 ps. I have found that just after reach equilibrium
> temperature my protein unfolds, but in a unexpected way. It seems
> extrange to me this behaviour, so I though I would be having a problem
> with temperature copntrol with berendsen and annealing. With that
> .mdp, what does the program exactly? rises temperature and then leaves
> the berendsen coupling at 500? or it uses another method? I am
> confused.
check temperatures with g_energy
no one knows what a protein looks like at 500 K in solvent
your tau_p is too short
>
> Leonardo
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--
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://xray.bmc.uu.se/~spoel
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