[gmx-users] Longer scale simulations

Ran Friedman ran at hemi.tau.ac.il
Wed Dec 10 12:41:01 CET 2003


Does this approach still confer some advantages compared to normal MD?

For example, can I use non-periodic boundary conditions in order to reduce computation time?



Berk Hess wrote:

> > > Regarding SD - is it possible to divide the system to a region were full
> >MD takes place and a region where SD is effective?
> >we can not combine these.
> They can be combined.
> You can use different friction constants for different groups of atoms.
> A very small friction produces results which are almost indistinguishable
> from MD.
> The only problem is that you should not have to much cut-off artifacts, as
> these might
> alter the temperature.
> But such an approach will not make the simulation faster, as the timestep
> will be limited
> by the MD part and unless the friction constant is very high, SD will not
> allow for larger
> timesteps then MD.
> Berk.
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Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university

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