[gmx-users] simulation in vacuum

Thomas Schlesier schlesi at uni-mainz.de
Thu Sep 18 12:24:33 CEST 2008

@ David: Thanks for the paper. (Patriksson et al. Biochemistry 46 pp.
933-945 (2007))
But how can I turn the Cut-Offs off?

Think it's best to describe first what I do:
I simulate pulling experiments of a small model system (consisting of
two ureas with short alkane linkers). In the future I want to simulate
two fixed chains which are connected by pairs of the small system and
look how the pairs open. (Simulations in solvent will follow, but to see
how it work, I think it is easier to start in vacuum).
|---X X---|
|              |
|---X X---|
|              |
|---X X---|

The system will look like that above (X are the ureas groups, which form
hydrogen bonds).
But first I want to simulate only one pair. The only way to use
(effective) no Cut-Off, would be that I use an very large Cut-Off so
that the molecules are all the time in it. But I think (after reading
the paper) there is another way to do this.

Regarding the protonating state, I think the molecules are not protonated.

Thanks for all the help.

More information about the gromacs.org_gmx-users mailing list