From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jul 13 2007 - 19:35:07 CDT
Why can't you define a coupling constant?
According to the manual, it seems if "langevinDamping" is not used,
it defaults to "langevinFile" which defaults to the coordinates
provided and the occupancy column of that pdb. The log file should
tell you exactly what it's doing in the beginning.
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node30.html
On Jul 13, 2007, at 6:53 AM, Philipp Schön wrote:
> dear users
> i do a temperature gradient running the following commands (it is
> similar with tCouple):
> for { set temperature 300 } { $temperature <= 400 } { incr
> temperature 10 } {
> if {$temperature < 400} {
> langevinTemp $temperature
> run 500
> } else {
> langevinTemp $temperature
> run 50000
> }
> }
> my question: since one cannot define a coupling constant when doing
> this (since an extra pdb file is provided to thermalize the specfic
> atoms in column B) how large is it? that is a black box and i
> really would like to know it.
> concerning berendsen et al. the is a threshold value and one should
> not go below it since potential energy effects become dominant.
> regards
> philipp
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