[gmx-users] Dihedral PCA documentation

[Anna Vernon]

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


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 outdated.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
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