[gmx-users] Loop refirement using simulated annealing

James Starlight jmsstarlight at gmail.com
Tue May 27 22:11:42 CEST 2014

Dear Gromacs users!

I need to refine some flexible regions (mainly long loop and linker
regions) of my proteins prior to the production MD run using some enhanced
sampling workflow applicable to the selected protein regions.  I  suppose
that force field based simulated annealing using Langevens dynamics as the
thermostat and positions restraints applied to the all protein atoms but
not for loops for which I'd like to find native-like conformations is
exactly what I look for. Could someone suggest appropriate SA setups for
such task: e.g number of SA windows, coupling constants in each windows,
appropriate implicit solvent models?



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