Hi,
if you give g_sdf just one molecule (in mode 1) to look at the
distribution of other atoms around it, everything looks fine. However,
if you give two or more molecules, the refmol.gro that is printed is
messed up, but the actual density map still looks ok. You can try this
with the 216 water molecule tutorial case.
Run a short md writing frames into traj.xtc.
Append these lines to the index.ndx (which has only OW group before these).
[ O1 ]
1 4
[ H1 ]
2 5
[ H2 ]
3 6
or
[ O1 ]
1
[ H1 ]
2
[ H2 ]
3
give
g_sdf -s topol.tpr -f traj.xtc -n index.ndx -r
2
3
4
1
and have a look at the refmol.gro in the two cases.
Is there something wrong in adding up the coordinates?
Cheers,
Atte
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