AMBER Archive (2005)

Subject: AMBER: langevin, GB and simulated annealing - 4

From: pascal.baillod_at_epfl.ch
Date: Tue Apr 26 2005 - 10:23:20 CDT

Thank you very much for your answer. Unfortunately, the input file I sent you
does not do that for langevin dynamics. The temperature just shoots up to 300 K
instead of staying around 0 or rising slowly. That same input file works with a
berendsen thermostat however. That's why I ask if the 2 options langevin and
temperature change (such as I have posted - which is the syntax for simulated
annealing) cannot be used together..

Thanks for your help.

Pascal

Quoting David Case <case_at_scripps.edu>:

> On Tue, Apr 26, 2005, pascal.baillod_at_epfl.ch wrote:
>
> > To use Langevin dynamics, you could set a series of target
> temperatures,
> > (say 600, 500, 400, 300, 200, 100, 10, etc.) to take effect at
> different times
> > during the simulation. This could have the effect of fairly slow
> cooling.
> > But the Berendsen approach seems to me to be a more natural way of
> carrying
> > out simulated annealing.
> >
> > Practically speaking, you mean there would be one simulation for each
> of
> > these temperatures, so that in the end I would have to paste the
> trajectory
> > and energy files? Or are there any tools to do that in one single
> simulation
> > in amber?
>
> You can easily set the target temperature to be different at different
> times
> during the simulation. In fact, the input file you posted does this:
>
> > &wt
> > TYPE='TEMP0', istep1=0, istep2=400000, value1=0.0,
> value2=300.0,
> > &end
> > &wt
> > TYPE='TEMP0', istep1=400001, istep2=32000000, value1=300.0,
> value2=300.0,
> > &end
>
> ...dac
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

*******************************************************************************
Pascal Baillod (PhD student)
*******************************************************************************
Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry pascal.baillod_at_epfl.ch
Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch
CH-1015 Lausanne
*******************************************************************************
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu