[gmx-users] pulling with dodecahedral box

Mareike Zink mzink at gwdg.de
Thu May 24 11:16:20 CEST 2007


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?


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