[gmx-users] extra points wrapping in trajectory

Lubos Vrbka shnek at tiscali.cz
Thu Aug 4 18:05:57 CEST 2005

hi guys,

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...

best regards,

_ at _"

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