[gmx-users] Re: How to calculate dihedral angle ??

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> HI
> I use   mk_angndx   to     produce      angle.ndx
> then, enter  g_angle -od angdist.xvg -ov angaver.xvg -type dihedral
>
>
> it follows the options:
> Group     0 (Phi=180.0_2_70) has     4 elements
> Group     1 (Phi=180.0_2_6) has    16 elements
> Group     2 (Phi=180.0_2_40) has   192 elements
> Select a group:
>
>
> what does the file angle.ndx mean?
>   

I suggest reading the manual regarding index files.

> what are the three groups represent ?
>   

Whatever you told mk_angndx when you created the file.

> which group should I pick up?
>   

Whichever one(s) you want to analyze.

-Justin

>
>
> this is the angle.ndx
> what does it mean??
> [ Phi=180.0_2_70 ]
>     11    12    13    14
> [ Phi=180.0_2_6 ]
>      7    11    12    13     9    11    12    13    12    13    14    15
>     12    13    14    17
> [ Phi=180.0_2_40 ]
>      2     1     3     4     2     1     3     7     5     1     3     4
>      5     1     3     7     4     3     7     8     1     3     7     8
>      1     3     7    11     4     3     7    11     8     7    11    12
>      3     7    11     9     8     7    11     9     3     7    11    12
>      7    11     9     5     7    11     9    10    12    11     9     5
>     12    11     9    10    11     9     5     1    11     9     5     6
>     10     9     5     1    10     9     5     6     9     5     1     3
>      9     5     1     2     6     5     1     3     6     5     1     2
>     13    14    15    16    13    14    15    19    17    14    15    16
>     17    14    15    19    14    15    19    23    14    15    19    20
>     16    15    19    23    16    15    19    20    15    19    23    21
>     15    19    23    24    20    19    23    21    20    19    23    24
>     19    23    21    17    19    23    21    22    24    23    21    17
>     24    23    21    22    23    21    17    14    23    21    17    18
>     22    21    17    14    22    21    17    18    21    17    14    15
>     21    17    14    13    18    17    14    15    18    17    14    13
>
>
>
> Thanks
>
> Lin
>
>
>
>
>
>
> Message: 2
> Date: Mon, 30 Jun 2008 16:39:17 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] How to calculate dihedral angle ??
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <48694475.6000506 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Chih-Ying Lin wrote:
>   
>> HI
>> g_chi is designed to help user to calculate the dihedral angles.
>>
>> I have an organic compound and as the manual describes that .gro ,
>> .trr  and ssdump.dat are the required input files to compute and
>> collect the dihedral angles with time.
>>
>>     
>
> g_chi is for use with the peptide backbone, according to the
> documentation, so I don't know how applicable it necessarily is to your
> situation.
>
> You might be better off using g_angle with an appropriate index group
> for the dihedral(s) of interest.  I have had success using it with small
> organic molecules.
>
> -Justin
>
>   
>> For my case, .gro and .trr files are ready.
>> How to prepare for ssdump.dat?
>>
>>
>> Also, how do i tell gromacs the calculate the specific dihedral angles
>> with time for me??
>> I did not fully understand the manual's description.
>>
>> thank you
>>
>> Lin
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>   

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

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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