[gmx-users] Qeustion on use of freeze groups for solid walls
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 11 09:50:59 CEST 2004
On Tue, 2004-05-11 at 02:44, Daejoong Kim wrote:
> Hi all.
> I am trying to simulate interactions with solid walls and solvents, which I
> think is kind of common. For that I want the wall to be fixed in space and I
> think a "freeze group" is a right one to use. But still I want to include
> van Der Waals interactions for solvent atoms due to these walls. Does the
> atom within "freeze groups" can act an van der Waals interactions to any
> other atoms other than the one within the same group?
You can just make a crystal like wall and freeze it. There will be VDW
interactions unless you turn them off explicitly (with energy_exclusions
in the mdp file).
> Thanks in advance.
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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