[gmx-users] how heat and deform a structure?

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 14 21:01:07 CET 2001

On Fri, 14 Dec 2001, Geraudis Mustelier wrote:

>I would like to do a simulated annealing but I have a doubt. If I do not
>want to begin the simulated annealing from the original conformation, hence,
>to deform the structure previously. Perhaps, to heat the structure little by
>little until taking it a new conformation, then starting from this new
>structure the simulated annealing. The objective is to explore other
>structure's conformations and, if it is possible, to verify if among the
>obtained conformations (local energetic minimum) repeats the original
>Is this possible? How can make it?
Best you do a normal MD simulation, maybe at slightly elevated
temperature, say for 2 ns, and then take snapshots every 500 ps which you
use starting point for new simulations. It could be interesting to compare
the resulting trajectories using essential dynamics analysis (g_covar,

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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