[gmx-users] g_densmap options and use

[Mark Abraham]

On 13/11/2010 4:07 AM, sa wrote:
> 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 ? 

Doesn't g_densmap -h explain the three groups?

> 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 ?)

Probably badly-formed input is silently breaking something somewhere.

Mark