[gmx-users] pulling with dodecahedral box

Tsjerk Wassenaar tsjerkw at gmail.com
Thu May 24 21:18:18 CEST 2007

Hi Mareike,

Probably your simulation starts off with remapping your pull-atom over
the periodic boundaries. Make sure that the atom and the protein are
properly placed inside the rhombic dodecahedron (actually the brick
representation of it) before the simulation. Note that Gromacs
performs mapping based on the first atom of each molecule, so if you
center the protein and the pull-group according to the first atom of
each, you should be fine.



On 5/24/07, Mareike Zink <mzink at gwdg.de> wrote:
> Hallo!
> I have got a question on the afm pulling option. I am trying to pull a single
> atom into the direction of the center of mass of a protein in my simulation
> cell. Everything works fine with a cubic box. When I use a truncated
> dodecahedral box, at time step 1 the atom is suddenly located at a comlete
> different position as in step 0 and the pulling direction is therefore wrong
> as well. Nevertheless, the force is 0 at step 0, so I expect the spring
> constant to be in the right position and my afm_init is okay. Has anyone any
> experience with pulling in dodecahedral boxes and can help me, please?
> Thanx,
> Mareike
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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