Hi, I am running MD simulation in approximately 1.25x1.25x1.25 nm box containing 64 waters and one LiF ion pair in NpT ensemble using gromacs 4.5.5 version. I am constraining the distance between ions using pull code and printing out force:
; COM PULLING pull = constraint pull_geometry = distance pull_group0 = LI pull_group1 = F pull_start = no pull_init1 = 0.225 The distance between ions in initial condition is 0.223 nm. After running grompp, I obtained the following error message: Distance of pull group 1 (0.610737 nm) is larger than 0.49 times the box size (0.387133) None of the reported numbers is correct. If I exchange LI and F, i.e. ; COM PULLING pull = constraint pull_geometry = distance pull_group0 = F pull_group1 = LI pull_start = no pull_init1 = 0.225 .tpr file can be created and simulation runs for a while, but it crashes with similar error message. Input files that I used are attached, simulation runs without problems in version 4.0.7. I've found similar report about this problem http://lists.gromacs.org/pipermail/gmx-users/2011-March/059398.html but it remained unanswered. Best regards, Eva
conf.in.gro
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grompp.mdp
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index.ndx
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topol.top
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