[gmx-users] Question about annealing and thermostat

[David]

On Wed, 2005-08-31 at 13:46 -0400, Leonardo Sepulveda Durán 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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