[gmx-users] g_sdf reference configuration question

[Matt Wyczalkowski]

I'm getting odd behavior with the reference configuration generated by
g_sdf (v. 3.3.3).  I am wondering if this is a bug, and if the spatial
density profile is similarly affected.

My test system has simple, regular geometry: a glycine 15-mer held
frozen in a fully extended "rod-like" configuration, with water
solvent.  I wish to evaluate, for instance, the spatial distribution
of water O around the 15 instances of the glycine O.  My understanding
is that g_sdf will average the water oxygen SDF around the 15 sites to
yield one composite SDF -- is this correct?

However, the reference configuration, given by g_sdf -r, seems
incorrect when performing the SDF around more than one atom triplet.
Based on the documentation, Atom 1 (the GLY O) should be at the
origin, and Atom 2 (GLY C) should be offset along the Z-axis only.
When there is only one atom triplet (that is, performing sdf around
just one GLY O), this is in fact the case.  However, when performing
an SDF around more than one atom, this is no longer holds, and the
offset increases with increasing number of triplets.

Below I give the output of three reference .gro files illustrating
this.  In all cases, Atom 1 is GLY O, Atom 2 is GLY C, Atom 3 is GLY
CA; Atom 4 is Water OW.

My question is, first, should I expect the GLY O to lie at the origin
in all instances? Is this a bug, or user error?  And if this is a bug,
are the sdf data reliable?

Regards,

Matt
---
Matt Wyczalkowski
Doctoral Candidate, Biomedical Engineering
Pappu Lab: http://lima.wustl.edu
Washington University in St. Louis


Reference Configuration .gro files:
(constructed with, e.g.  g_sdf -f ../traj.xtc -n index-all.ndx -s
../GLY15Frozen.tpr -o OO-all -r OO-all -grid 2 2 2 -b 500 )

For one GLY residue:
Protein
  7
    4  GLY    N    1   0.187   0.033  -0.090
    4  GLY    H    2   0.041   0.046  -0.090
    4  GLY   CA    3  -0.000   0.193  -0.089
    4  GLY  HA1    4   0.086   0.281  -0.088
    4  GLY  HA2    5   0.243   0.119  -0.091
    4  GLY    C    6  -0.000   0.000  -0.179  ;  OFFSET ALONG Z AXIS
    4  GLY    O    7   0.000   0.000   0.000   ;  AT ORIGIN
   10.00000   10.00000   10.00000


For two GLY residues:
Protein
  7
    4  GLY    N    1   0.575  -0.257  -0.087
    4  GLY    H    2   0.430  -0.244  -0.086
    4  GLY   CA    3   0.389  -0.097  -0.088
    4  GLY  HA1    4   0.474  -0.009  -0.089
    4  GLY  HA2    5   0.632  -0.171  -0.090
    4  GLY    C    6   0.388  -0.291  -0.175
    4  GLY    O    7   0.389  -0.288   0.005   ; NOT AT ORIGIN
   10.00000   10.00000   10.00000

For all 15 GLY residues:
Protein
  7
    2  GLY    N    1  -1.438   1.227  -0.102
    2  GLY    H    2  -1.551   1.280  -0.097
    2  GLY   CA    3  -1.631   1.377  -0.104
    2  GLY  HA1    4  -1.595   1.400  -0.112
    2  GLY  HA2    5  -1.421   1.256  -0.109
    2  GLY    C    6  -1.572   1.263  -0.123
    2  GLY    O    7  -1.564   1.272  -0.064  ; NOT AT ORIGIN
   10.00000   10.00000   10.00000