[gmx-users] Dihedral PCA documentation

Tue Feb 28 03:58:14 CET 2017

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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>>>>>
>>>
>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================