[gmx-users] Simulation in the high temperature conditions

James Starlight jmsstarlight at gmail.com
Tue Apr 3 11:14:51 CEST 2012

Dear Gromacs users!

I want to perform simulation of the membrane protein in the
Ccl4-membrane-mimicking interiour in the increaced ( up to 600 K)
temperature on the nvt ensemble.

As the consequence I'd like to protect the temperature caused
destabilisation of my protein and simulate native-like conformation events
in the speed-up manner.

What should I use for preparing of my system? As I understtod I neen long
nvt equilibration phase prior to productive run to addaptate my system to
the uncommon conditions. For this I want to perform step-by-step increasing
of the Ref_T for all separate groups of my system ( Protein_Ccl4,
Water_Ions ). E.g I'll separate my equilibration phase on the 20 steps with
the ref_t 310, 320, 330... 600K and the length of each step 50ps. Could
this aproach could be usefull? What addition tricks could I use ( e.g
dynamics of changing tau_t for different groups etc)?

Thanks for help,

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