[gmx-users] Dihedral PCA documentation
Anna Vernon
lappala.anna at gmail.com
Tue Feb 28 05:51:29 CET 2017
Thank you Justin,
that makes sense, thank you for help. However, I am struggling with the
rest, due to lacking documentation & examples. Like Alex said, this
web-page http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA is
outdated, but there is no new version of it available... Or at least I
am not finding it (and I have noticed that people on the list have asked
questions similar to mine, but there were no answers to any of my
questions, sadly).
mk_angndx -s h3_md.tpr -n h3_ANGLE.ndx -type dihedral
is what I now have done, and my next steps should be the following, I guess,
trjconv -s h3_md.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0
but I do not have a trr file because mk_angndx does not generate it
(unlike the old documentation command angle) and again, my tpr file
contains waters, not just the molecule of interest that I have in my
.gro file. I also do not understand the difference between the
dangle.ndx file and covar.ndx file... What is resized.gro? It would be
really helpful to write out those explanations in documentation and
perhaps give a more realistic example because this really becomes
frustrating.
Thanks for your time & help, it is very much appreciated.
Anna
On 27/02/17 19:58, Justin Lemkul wrote:
>
>
> On 2/27/17 9:55 PM, Anna Vernon wrote:
>> Thanks Justin,
>>
>> but I did use this command, which is supposed to be dihedral:
>>
>> g_angle -f h3_nowater.gro -n h3_ANGLE.ndx -or h3_ANGLE.trr -type
>> dihedral
>>
>
> Sure, but g_angle is only going to give you the options presented to
> it in the index file. If those groups were created incorrectly (note
> my comments were about mk_angndx, not g_angle) then you have to create
> them properly. You can't get dihedrals from valence angles :)
>
> -Justin
>
>> thanks
>>
>> A
>>
>>
>> On 27/02/17 19:35, Justin Lemkul wrote:
>>>
>>>
>>> On 2/27/17 9:29 PM, Anna Vernon wrote:
>>>> Thanks Alex.
>>>>
>>>>
>>>> tried the new syntax, below the output of g_angle, which did not
>>>> get any
>>>> easier... Хрень осталась...)))
>>>>
>>>> Group 0 (UB_th=108.4_297.062f) has 36 elements
>>>> Group 1 (UB_th=108.9_384.092f) has 30 elements
>>>> Group 2 (UB_th=109.7_794.962f) has 6 elements
>>>> Group 3 (UB_th=111.5_376.562f) has 6 elements
>>>> Group 4 (UB_th=110.1_221.752f) has 36 elements
>>>> Group 5 (UB_th=109.0_297.062f) has 33 elements
>>>> Group 6 (UB_th=109.5_430.952f) has 36 elements
>>>> Group 7 (UB_th=113.5_585.762f) has 12 elements
>>>> Group 8 (UB_th=121.0_376.562f) has 12 elements
>>>> Group 9 (UB_th=119.5_351.462f) has 24 elements
>>>> Group 10 (UB_th=124.0_669.442f) has 12 elements
>>>> Group 11 (UB_th=112.5_167.362f) has 12 elements
>>>> Group 12 (UB_th=121.0_669.442f) has 15 elements
>>>> Group 13 (UB_th=109.5_276.142f) has 30 elements
>>>> Group 14 (UB_th=107.0_418.402f) has 12 elements
>>>> Group 15 (UB_th=112.2_365.682f) has 6 elements
>>>> Group 16 (UB_th=109.5_271.122f) has 6 elements
>>>> Group 17 (UB_th=109.5_271.122f) has 12 elements
>>>> Group 18 (UB_th=110.0_365.682f) has 3 elements
>>>> Group 19 (UB_th=111.0_292.882f) has 6 elements
>>>> Group 20 (UB_th=112.2_338.902f) has 3 elements
>>>> Group 21 (UB_th=111.0_359.822f) has 6 elements
>>>> Group 22 (UB_th=108.0_401.662f) has 6 elements
>>>> Group 23 (UB_th=110.1_288.702f) has 6 elements
>>>> Group 24 (UB_th=115.2_443.502f) has 6 elements
>>>> Group 25 (UB_th=107.5_433.462f) has 6 elements
>>>> Group 26 (UB_th=120.0_383.252f) has 12 elements
>>>> Group 27 (UB_th=120.0_334.722f) has 36 elements
>>>> Group 28 (UB_th=120.0_251.042f) has 60 elements
>>>> Group 29 (UB_th=110.1_279.742f) has 18 elements
>>>> Group 30 (UB_th=105.8_351.462f) has 3 elements
>>>> Group 31 (UB_th=112.1_343.092f) has 6 elements
>>>> Group 32 (UB_th=116.5_418.402f) has 3 elements
>>>> Group 33 (UB_th=122.5_627.602f) has 3 elements
>>>> Group 34 (UB_th=120.0_418.402f) has 6 elements
>>>> Group 35 (UB_th=120.0_192.462f) has 3 elements
>>>>
>>>
>>> These are Urey-Bradley angles with the given equilibrium angles and
>>> force
>>> constants. If you're using mk_angndx to create the index group, you
>>> want
>>> "-type dihedral" instead of "-type angle" (which is the default).
>>>
>>> -Justin
>>>
>>>>
>>>> On 27/02/17 16:04, Alex wrote:
>>>>> I think you might be referring to the 2010 version of the online
>>>>> manual (
>>>>> http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA), which
>>>>> is pretty
>>>>> outdated. A lot of syntax seems to be changing fairly rapidly, so
>>>>> хрень
>>>>> like this is to be expected. ;)
>>>>> The current manual points to gmx angle, gmx covar and, gmx anaeig for
>>>>> covariance analysis, and for those the updated help pages are
>>>>> separate:
>>>>> http://manual.gromacs.org/programs/gmx-angle.html
>>>>> http://manual.gromacs.org/programs/gmx-covar.html
>>>>> http://manual.gromacs.org/programs/gmx-anaeig.html
>>>>>
>>>>> Alex
>>>>>
>>>>> On Mon, Feb 27, 2017 at 3:44 PM, Anna Lappala
>>>>> <lappala.anna at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear Gromacs users,
>>>>>>
>>>>>> The documentation on Dihedral PCA analysis is confusing.
>>>>>>
>>>>>> Firstly, the links are redirecting to the main gromacs page
>>>>>> which does
>>>>>> not help because one needs to search for the specific commands
>>>>>> from there.
>>>>>>
>>>>>> Secondly, -s option does not work in step 2: invalid command line
>>>>>> argument
>>>>>> "-s".
>>>>>>
>>>>>> Thirdly, my tpr file contains water which I do not want to
>>>>>> include in the
>>>>>> analysis, how can I change that?
>>>>>>
>>>>>> .ndx file output produced by mk_angndx is a mess- first line, for
>>>>>> example,
>>>>>> is [UB_th=108.4_297.062f]
>>>>>>
>>>>>> I need a small number of dihedrals, so I could write the file
>>>>>> myself but
>>>>>> there again is no clear explanation how to do it: the [foo] 1 2 3
>>>>>> 4 example
>>>>>> could be expanded- do I use "dihedrals" instead of foo? Or
>>>>>> filename? Or
>>>>>> molecule name?
>>>>>>
>>>>>> Finally, I would really appreciate it if someone could give an
>>>>>> explanation
>>>>>> or a clear example of how this works, for a simple system or a
>>>>>> protein,
>>>>>> because documentation is unclear to me.
>>>>>>
>>>>>> Kind regards,
>>>>>> Anna
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
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>>>>>>
>>>>
>>>
>>
>
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