[gmx-users] Re: Simulation in the high temperature conditions

James Starlight jmsstarlight at gmail.com
Wed Apr 4 13:25:48 CEST 2012

So if it were not quite clearly :)

 my main question is about methodology of such gradually temperature rise
in the nvt enssemble conditions. Might it be realised by means of simple
equilibation in one mdp file varying some parametries to change time-step
of temperature growth? Or this methodology require several mdp files with
slightly different ref_t as well as gen_temp options ? Finally what exactly
is tau_t time constant?


3 апреля 2012 г. 13:14 пользователь James Starlight
<jmsstarlight at gmail.com>написал:

> 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,
> James
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