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... Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
