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

[Chih-Ying Lin]

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?
what are the three groups represent ?
which group should I pick up?



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

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