[gmx-developers] Re: Welcome to the "gmx-developers" mailing list

[David van der Spoel]

On Mon, 11 Aug 2008, JMandumpal wrote:

>
>  Dear GROMACS developers,
>
>                              In order to measure the glass transition
>temperature of water and aqueous solutions with different cooling rates, 
>Stanley et al have reported a modified NVT simulation - Physical Review
>Letters 93, 2004 047801-1.
>
>His method is as follows:
>
>The simulation is run in the NVT ensemble. The temperature during the
>simulation, ref_T, is controlled by using a Berendsen thermostat .
>
>In a standard NVT simulation, To is constant. In their cooling/heating
>simulations,  Berendsen thermostat is used but, at everytime step, they
>also update the bath temperature ref_T such that
>
>ref_T= ref_T - deltaT, with deltaT= cooling/heating rate *  timestep.
>

this is called simulated annealing. check mdp options.
you don't have to change any code.

>This is done at every time step before rescaling the velocities.
>
>
>In my case, I want to employ a cooling rate of -3*10^10 K/fs and time
>step is 1 fs.
>
>that is delta T is -0.00003K/fs
>
>and ref_T has to be updated at everytime step using the equation,
>
>ref_T= ref_T - 0.00003 -----------> eq.1
>
>
>How can I do this in GROMACS 3.3.3?
>
>I mean which file should I modify before compiling again;
>
>I checked md.c, do_gt.c and coupling.c  in 3.3.3/src/kernel but got
>confused as to find the line where I could impliment eq.1.
>
>I really hope that any of you can help me in this regard.
>
>
>regards,
>Jes
>
>
>
>
>
>
>
>

David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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