[gmx-users] contacts per residue in g_mindist

serena leone serena.leone at unina.it
Thu Nov 13 16:04:50 CET 2014

Dear GMX Users,

I have been trying to analyze the evolution of hydrophobic contacts
during an unfolding simulation. To do this, I have prepared an index
file with the hydrophobic residues in the two portions of the protein
that I simulated and I issued g_mindist as follows:

g_mindist -f prot.xtc -s prot.tpr -d 0.56 -o atm-pair_hydrophobic -on
numcont_hydrophobic -or mindistres_hydrophobic.xvg -n protein.ndx -dt 10
-printresname -respertime -od mindist_hydrophobic.xvg

If I understood correctly, atm-pair_hydrophobic gives me the atom
couples that are closest per frame according to their numbering in the
topology, whereas mindistres_hydrophobic.xvg with -respertime gives me
the evolution of the minimum distance between each residue in group 1 of
my analysis with the COM of group 2 of my analysis. Now the two

1) the mindistres_hydrophobic.xvg file that i open with grace has
several data sets in it, but the legend looks something like:

@ legend length 2
@ s0 legend "helix_hydrophobic-34-90_hydrophobic"
# PRO9 PHE10 LEU14 GLY15 PHE17 ALA18 VAL19 ILE25 

The numbering of the residues has been (i believe) taken from the
topology when I made the index, but this numbering is wrong, the
numbering in the structure file is exactly n+1 (i.e. PRO10 PHE11
LEU15...). If I visually analyze the corresponding .gro file, the
numbering is correct, coherent with the starting pdb, and most important
it is correct in every other ndx generated for instance by g_bonds,
index making and so on. Does anybody have any idea on why they appear
shifted in this case?

2)is there any way to extract the distance of the residue in group 1 not
from the COM of group 2, but from individual residues in it? in other
words, a sort of hbonds-style contact map with an index?

As a minor issue, I assume that PRO9 etc. are the data series names, but
they do not automatically appear on the plot (in grace). Although I can
fix this by hand, it might become pretty tedious if the groups become
bigger. Any hint on how to solve it? 

Thanks everybody and have a great day,

Serena Leone, PhD
Department of Chemical Sciences
University of Naples "Federico II"
Complesso Universitario Monte S. Angelo Via Cintia,4
I-80126 Naples, Italy
Phone (+39) 081 674242
Fax (+39) 081 674090

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