AMBER Archive (2005)

Subject: Re: AMBER: langevin, GB and simulated annealing - 5

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon May 09 2005 - 14:58:57 CDT

Pascal,
I finally got time to check the code and you're right, there is a
variable used
for temperature in Langevin dynamics that does not get updated during
the MD run.
This means that weight changes to TEMP0 have no effect for ntt=3.
I tested a fix and it works, we'll get a bugfix done as soon as I can
generate it. I'll mail you a modified sander.f if you want (off the list
to save
everyone's mailbox).
Carlos
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

pascal.baillod_at_epfl.ch wrote:

>Hello,
>
>Could anybody tell me how temeprature control is performed, when using a
>Langevin thermostat in amber8? I suppose that it is implemented as described in
>van Gunstern et al., 1981, if I understand the manual correctly. The temperature
>control would in this case be derived from the random collision force, that is
>taken from a temperature dependant gaussian distribution.
>
>I suppose simulated annealing could be performed by slowly varying the
>temperature of the gaussian distribution yielding the random collision force?
>But I think that is not implemented, as my simulated annealing input file, that
>works fine for Berendsen thermostat md, doesn't work for a langevin thermostat md.
>
>Thank you very much in advance!
>
>Pascal
>
>
>

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