[gmx-users] How to selectively making temperature coupling
gmx3 at hotmail.com
Thu May 18 10:11:03 CEST 2006
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] How to selectively making temperature coupling
>Date: Thu, 18 May 2006 18:05:07 +1000
>Zhenting Gao wrote:
> > Hi gmx-users,
> > In this paper,
> > Ota, N. & Agard, D. A. (2005). Intramolecular signaling pathways
>revealed by modeling anisotropic thermal diffusion. Journal of Molecular
>Biology 351, 345-354.
> > A good methodology to find the intramolecular allosteric pathway,
>namely, ATD, is defined.
> > Basicly, ATD cooled the system to 10K, then, by temperature coupling to
>the resides that you are interested in, one may find the heat transfer
>pathway by monitoring the atom fluctuation.
> > And ATD is very useful to me, who want to find the allosteric regulation
>pathway of a protein.
> > But, concerning the temperature coupling, I did not know how to set
>temperature coupling to only on group, and set no temperature coupling to
>other groups. I guess to do this, I need to modify the temperature coupling
>segment in the mdp file, so could anyone help to to work this out.
>I don't think that is possible with the current implementation.
> > If I set ref_t to '0' for group 'not_178_179', the coupling is removed
> > ; Groups to couple separately
> > tc-grps = 178_179 not_178_179
> > ; Time constant (ps) and reference temperature (K)
> > tau_t = 0.1 0.1
> > ref_t = 300 0
>This will couple not_178_179 to a thermal bath at zero Kelvin, which is
>quite a bit different from coupling it to no bath at all. You could try
>just having 178_179 coupled and no coupling for the rest... My guess is
>that this would gradually bleed heat from the coupled group to the rest
>of the degrees of freedom of the system, so you'd end up with a
>poorly-coupled system at 300K. If the above investigators cooled the
>system to 10K, they probably continued to regulate the non-interesting
>parts of the system to that temperature...
You can not have no coupling for a group.
You could use near-infinite coupling time though, something like 10e12.
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