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" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] How to calculate dihedral angle ??
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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
========================================
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