[gmx-users] g_densmap options and use

[sa]

Dear All,

I would like to compute the average 2D density distribution of the water
around 6 peptides aggregated in the cluster within the simulation box with
gromacs, for that I think that g_densmap is the the good tool (correct ?).

However it is not very clear for how to use g_densmap. Below the command I
used with g_densmap (ver GMX 4.5.3)

g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr
-bin 0.02 -amax 30 -rmax 30 -b 0 -e 80000 -o 6_Peptide_53A6_densmap.xpm -od
6_Peptide_53A6_densmap.dat

When I use the above command, g_densmap asks me to choose two groups to
define the axis and an analysis group:

Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision)
Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision)
Select two groups to define the axis and an analysis group
Group     0 (         System) has 86359 elements
Group     1 (        Protein) has   546 elements
Group     2 (      Protein-H) has   396 elements
Group     3 (        C-alpha) has    48 elements
Group     4 (       Backbone) has   144 elements
Group     5 (      MainChain) has   192 elements
Group     6 (   MainChain+Cb) has   234 elements
Group     7 (    MainChain+H) has   246 elements
Group     8 (      SideChain) has   300 elements
Group     9 (    SideChain-H) has   204 elements
Group    10 (    Prot-Masses) has   546 elements
Group    11 (    non-Protein) has 85813 elements
Group    12 (          Other) has 17320 elements
Group    13 (            URE) has 17320 elements
Group    14 (             CL) has     6 elements
Group    15 (          Water) has 68487 elements
Group    16 (            SOL) has 68487 elements
Group    17 (      non-Water) has 17872 elements
Group    18 (            Ion) has     6 elements
Group    19 (            URE) has 17320 elements
Group    20 (             CL) has     6 elements
Group    21 ( Water_and_ions) has 68493 elements
Select a group: 1
Selected 1: 'Protein'
Select a group: 16
Selected 16: 'SOL'
Select a group: 16
Selected 16: 'SOL'

I chose protein and SOL, the program ask me to choose a third group (?) What
to choose ? I choose SOL again, the program computes something but i can not
inspect the results are what i want since no xpm is generated by g_densmap
(is this a bug ?)

Thank you for your help and your guidance

Stefane
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