[gmx-users] g_rdf and g_select for number of res with COM within distance to surface

[Patrick Charchar]

Hi all,

I'm trying to calculate the number of residues (part of a residue) within a
distance (0.5 nm) to the surface of a molecule.

The molecule (MOL) is made up of 43 atoms.
The residues of interest are ASP (there's 36 of them in my system), but I'm
only interested in the COM between OD1 and OD2 (i.e. the two side chain
oxygens).

So essentially I want the distance between the COM of each OD1/OD2 pair in
reference to any atom of MOL.

To achieve this I have used g_select and g_rdf at a single frame but the
answers differ and I'm not sure why. I'm using version 4.6.5, but I've
tested this on 5.0.5 and the same result is observed.

The lines of interest are:
g_select -f ../trjs/*nj.xtc -s ../../vel1/md-tpr/*struct.tpr -n
../index.ndx -select 'res_com of group ASP_oxygens and within 0.5 of group
MOL' -oi closeASP.dat -resnr index -b 0 -e 0

echo 140 139 | g_rdf -f ../trjs/*nj.xtc -s ../../vel1/md-tpr/*struct.tpr -n
../index.ndx -o -cn -rdf res_com -surf mol -b 0 -e 0

(where group 140 is ASP_oxygens and group 139 is MOL)

The output from g_select -oi is:
0.000    *7*   45   86  115  121  122  129  143

while from g_rdf -cn (at 0.5 nm) its:
0.5          *5*


So g_select says 7 residues are within 0.5 nm while g_rdf says 5 residues.

I've also tried at different frames, but always obtain different results
form the two tools and can't figure out why. Any insight would be
appreciated.

Cheers,
Patrick