[gmx-users] How to selectively making temperature coupling

Zhenting Gao zhentg at 163.com
Thu May 18 09:31:49 CEST 2006

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. 

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 

Longing for your kind reply soon. 

Yours sincerely,  
Zhenting Gao  
zhentg at mail.shcnc.ac.cn  
Drug Discovery and Design Center,  
Shanghai Institute of Materia Medica,  
Chinese Academy of Sciences  

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