[gmx-users] Longer scale simulations

Ran Friedman ran at hemi.tau.ac.il
Tue Dec 9 15:06:01 CET 2003

Dear GMX users and developers,

I'd like to simulate protein motions which will normally take longer than the scale of MD simulations.

Are such calculations feasible using the SD or BD algorithms in Gromacs?

Are you aware of any references to such calculations made using Gromacs?

Regarding SD - is it possible to divide the system to a region were full MD takes place and a region where SD is effective?

Thank you,


Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university

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