From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 18 2005 - 12:02:37 CST
If you want to apply the same coupling to all atoms (or even all
non-hydrogens), you don't need to specify a file and can instead use
the langevinDamping option. The units of this are the same as those
you can put in the file, 1/ps. The langevinFile option gives you more
control though. You can use any column, but you have to also use the
option langevinCol (O, B, etc.) to tell namd in which column to look.
On Nov 18, 2005, at 11:09 AM, curcio wrote:
> Hi,
>
> I have a question about the temperature coupling method as implemented
> in
> NAMD.
> In general to use this method the desired temperature has to be
> specified
> along with something like a coupling time and it is about the latter
> that I
> have a question.
> According to the NAMD user's guide it is possible to specify a
> "coupling
> coefficient" in one of the usual columns of a pdb-file but nothing is
> said
> there what this "coupling coefficient" is nor its unit is given (ps?
> 1/ps?).
> Does anyone know what I have to put in the pdb-file (any column) if I
> want to
> use a coupling time of say 5ps (for all atoms)? Is it simply 5.00?
>
> Thanks very much.
>
> Raffaele
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