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" <[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 > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== 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 ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php