[gmx-users] Dihedral PCA documentation

Tue Feb 28 03:55:32 CET 2017

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

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
>>>>
>>>> * Please search the archive at http://www.gromacs.org/
>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>
>