[gmx-users] Gmx gangle

Thu Dec 13 19:58:11 CET 2018

On 12/13/18 1:05 PM, rose rahmani wrote:
> Would you please answer my question? Did you check it?

We can't check your work for you because we don't know what output you 
got or why you are suspicious about it. The selections look sensible but 
if you ever question if something is working, you need to have a test 
case where you know the outcome. If the program doesn't produce the 
output you know to be right, likely your approach is wrong. If the 
output confirms your suspicions, then you're right.

-Justin

> 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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>> --
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-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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