[gmx-users] Gmx gangle

Thu Dec 13 19:05:54 CET 2018

Would you please answer my question? Did you check it?

On Wed, 12 Dec 2018, 02:03 Mark Abraham <mark.j.abraham at gmail.com wrote:

> Hi,
>
> I would check the documentation of gmx gangle for how it works,
> particularly for how to define a plane. Also, 4.5.4 is prehistoric, please
> do yourself a favor and use a version with the seven years of improvements
> since then :-)
>
> Mark
>
> On Tue., 11 Dec. 2018, 10:14 rose rahmani, <rose.rhmn93 at gmail.com> wrote:
>
> > 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 tiß¸ 4000.000
> >
> > Am I right? I don't think so. :(
> >
> > Would you please help me?
> > --
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