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