From: Mark Abraham <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
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
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...
You can not have no coupling for a group.
You could use near-infinite coupling time though, something like 10e12.
Berk.
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