[gmx-users] simulation in vacuum

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 18 12:17:22 CEST 2008

Thomas Schlesier wrote:
> @ David: Thanks for the paper. (Patriksson et al. Biochemistry 46 pp.
> 933-945 (2007))
> But how can I turn the Cut-Offs off?
Set them to zero.
And also nstlist = 0.

> 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.
> Thomas
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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