[gmx-users] How to selectively making temperature coupling
Mark.Abraham at anu.edu.au
Thu May 18 10:05:07 CEST 2006
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 or not?
> ; 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...
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