[gmx-users] Dihedral PCA documentation
jalemkul at vt.edu
Tue Feb 28 03:35:17 CET 2017
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).
> 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 outdated.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:
>> On Mon, Feb 27, 2017 at 3:44 PM, Anna Lappala <lappala.anna at gmail.com>
>>> 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
>>> 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,
>>> 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.
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
More information about the gromacs.org_gmx-users