[gmx-users] pulling with dodecahedral box
Mareike Zink
mzink at gwdg.de
Thu May 24 11:16:20 CEST 2007
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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