[gmx-users] Gmx gangle

Wed Dec 12 07:23:29 CET 2018

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.

Thank you so much Mark. As a GROMACS lover, I like to make a suggestion; I
think sth it would be REALLY helpful if you provide some proper examples
for gromacs tools, with results. You have straightforward tutorials and
useful manual, but some instructions in using tools, are a little ambiguous
and misleading. This also reduces the number of questions.

> Also, 4.5.4 is prehistoric, please
> do yourself a favor

I would like, but I remember that I wanted to use cutoff-scheme=group and i
couldnt come up with errors in gmx. These calculations are for more than
one year ago (and now I want some more analysis), i was a freshman,

> and use a version with the seven years of improvements
>
I was a freshman,  dear smiling man -:)

> since then :-)
>
I am waiting for you.

Best

>
> 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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