[gmx-users] g_spatial: merging solvent ond solute:::need some distance

[srinivasa rao lanke]

Dear sir,
congrats......and thank you very much for your kind replys..
................................................-------------------------------- 
 I fitted some group also
I tried whatever possible ways

1.water and water oxygen
2.groups and total system also

Even that group and SDF space overlapping in VMD view
.....................................................................................
some one suggested g_sdf is fine for this sdf calculation
i am using 4.6.3 version...but g_sdf is not available in this version.
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*
IN gromacs manual given one message.......

WARNINGS:
The SDF will be generated for a cube that contains all bins that have some
non-zero occupancy. However,
the preparatory -fit rot+trans option to trjconv implies that your system
will be rotating and
translating in space (in order that the selected group does not). Therefore
the values that are returned will
only be valid for some region around your central group/coordinate that has
full overlap with system volume
throughout the entire translated/rotated system over the course of the
trajectory. It is up to the user to ensure
that this is the case*

what is the meaning of these lines from manual ???.







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