[gmx-users] extra points wrapping in trajectory
shnek at tiscali.cz
Thu Aug 4 18:05:57 CEST 2005
i'm trying to view trajectory from gromacs using vmd. the system is a
slab with 6-center water molecules (O, H, H + 3 extra points). there is
one strange thing. after some time, the trajectory gets distorted - it
looks like extrapoints are not wrapped. when i display only oxygens and
hydrogens, then it's ok.
is it ok? i checked the files several times, but no hit. when displayed
in ngmx, it seems to be ok, however i'm not sure since extra points are
not connected to the "central" atom there...
this might be connected to the following as well. i don't use ewald,
since this water model is not parametrized for it. instead, i use
cutoff. it happens sometimes that one or several water molecules just
hang in free space (far from the slab) and don't move at all... that
sounds strange to me. i know that the distance to the slab is larger
than cutoff, but what about thermal motion?
has anyone encountered this? thank you in advance for any hint...
_ at _"
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