[gmx-users] Pull error message

[eva.pluharova at marge.uochb.cas.cz]

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






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