[gmx-users] Distance computation using g_mindist

[sunita at chem.iitb.ac.in]

Dear gmx-users,

In the manual it is mentioned that g_mindist computes the distance between
one group and a number of other groups. Does it calculates the minimum
distance between the center of mass of of one group with that of other for
a given time or it computes all possible distances between a pairs of
atoms in the specified groups at a given time and give the minimum
distance out of it.


Another question is that I have calculated the distance between amide
proton as one group and SOL as another group. The .xvg file shows the time
vs distance graph. The atm-pair.out file gives the atom id of
corresponding groups at a given time. From there I found that distance is
not between the NH proton but from N atom to HW1 of SOL though I had
specified explicitly one group as amide proton. Randomly I checked the
id's of SOL and it is always the HW1 but not HW2 or OW.Could I know how
does g_mindist program selects the index groups.