[gmx-users] Gmx gangle

[rose rahmani]

Hi,

I don't really understand how gmx gangke works!!!

I want to calculate angle between amino acid ring and surface during
simulation.
 I mad3 an index for 6 atoms of ring(a_CD1_CD2_CE1_CE2_CZ_CG) and two atoms
of surface. Surface is in xy plane and amino acid is in different Z
distances.


I assumed 6 ring atoms are defining a pkane and two atoms of surface are
defining a vector( along  Y). And i expected that the Average angle between
this plane and vector during simulation is calculated by gmx gangle
analysis.

 gmx gangle -f umbrella36_3.xtc -s umbrella36_3.tpr -n index.ndx -oav
angz.xvg -g1 plane -g2 vector -group1 -group2

Available static index groups:
 Group  0 "System" (4331 atoms)
 Group  1 "Other" (760 atoms)
 Group  2 "ZnS" (560 atoms)
 Group  3 "WAL" (200 atoms)
 Group  4 "NA" (5 atoms)
 Group  5 "CL" (5 atoms)
 Group  6 "Protein" (33 atoms)
 Group  7 "Protein-H" (17 atoms)
 Group  8 "C-alpha" (1 atoms)
 Group  9 "Backbone" (5 atoms)
 Group 10 "MainChain" (7 atoms)
 Group 11 "MainChain+Cb" (8 atoms)
 Group 12 "MainChain+H" (9 atoms)
 Group 13 "SideChain" (24 atoms)
 Group 14 "SideChain-H" (10 atoms)
 Group 15 "Prot-Masses" (33 atoms)
 Group 16 "non-Protein" (4298 atoms)
 Group 17 "Water" (3528 atoms)
 Group 18 "SOL" (3528 atoms)
 Group 19 "non-Water" (803 atoms)
 Group 20 "Ion" (10 atoms)
 Group 21 "ZnS" (560 atoms)
 Group 22 "WAL" (200 atoms)
 Group 23 "NA" (5 atoms)
 Group 24 "CL" (5 atoms)
 Group 25 "Water_and_ions" (3538 atoms)
 Group 26 "OW" (1176 atoms)
 Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms)
 Group 28 "a_320_302_319_301_318_311" (6 atoms)
 Group 29 "a_301_302" (2 atoms)
Specify any number of selections for option 'group1'
(First analysis/vector selection):
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> 27
Selection '27' parsed
> 27
Selection '27' parsed
> Available static index groups:
 Group  0 "System" (4331 atoms)
 Group  1 "Other" (760 atoms)
 Group  2 "ZnS" (560 atoms)
 Group  3 "WAL" (200 atoms)
 Group  4 "NA" (5 atoms)
 Group  5 "CL" (5 atoms)
 Group  6 "Protein" (33 atoms)
 Group  7 "Protein-H" (17 atoms)
 Group  8 "C-alpha" (1 atoms)
 Group  9 "Backbone" (5 atoms)
 Group 10 "MainChain" (7 atoms)
 Group 11 "MainChain+Cb" (8 atoms)
 Group 12 "MainChain+H" (9 atoms)
 Group 13 "SideChain" (24 atoms)
 Group 14 "SideChain-H" (10 atoms)
 Group 15 "Prot-Masses" (33 atoms)
 Group 16 "non-Protein" (4298 atoms)
 Group 17 "Water" (3528 atoms)
 Group 18 "SOL" (3528 atoms)
 Group 19 "non-Water" (803 atoms)
 Group 20 "Ion" (10 atoms)
 Group 21 "ZnS" (560 atoms)
 Group 22 "WAL" (200 atoms)
 Group 23 "NA" (5 atoms)
 Group 24 "CL" (5 atoms)
 Group 25 "Water_and_ions" (3538 atoms)
 Group 26 "OW" (1176 atoms)
 Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms)
 Group 28 "a_320_302_319_301_318_311" (6 atoms)
 Group 29 "a_301_302" (2 atoms)
Specify any number of selections for option 'group2'
(Second analysis/vector selection):
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> 29
Selection '29' parsed
> 29
Selection '29' parsed
> Reading file umbrella36_3.tpr, VERSION 4.5.4 (single precision)
Reading file umbrella36_3.tpr, VERSION 4.5.4 (single precision)
Reading frame       0 time    0.000
Back Off! I just backed up angz.xvg to ./#angz.xvg.1#
Last frame      40000 time 4000.Ö00
Analyzed 40001 frames, last ti߸ 4000.000

Am I right? I don't think so. :(

Would you please help me?