On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Amit Choubey wrote: > >> Hi Mark, >> >> That is true. But what does the manual refer to when it says >> the first graph is the average, the rest are the individual angles >> >> what and where are the rest? I am only curious because there might be a >> hidden feature that could be useful for me. >> >> > Read all of the help information; the command in the .xvg file below shows > that you're not yet using the right output options. Hint: look at the > sentence in g_angle -h before the one quoted above, as well as the -ov > flag... > -ov flag gives the average value of angle of the group with time. This is not very useful for me right now. I am interested in the distribution of dihedrals with angle. I was just curious about the -all features... > > -Justin > > Amit >> >> >> On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham >> <mark.abra...@anu.edu.au<mailto: >> mark.abra...@anu.edu.au>> wrote: >> >> Amit Choubey wrote: >> >> Hi Mark, >> >> Ok here is the command line i used :- >> >> g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e >> 804 -all >> output is >> # This file was created Tue Dec 1 20:20:41 2009 >> # by the following command: >> # g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e >> 804 -all >> # >> # g_angle is part of G R O M A C S: >> # >> # Go Rough, Oppose Many Angry Chinese Serial killers >> # >> @ title "Dihedral Distribution: C34_C36_C37_C38" >> >> >> This title makes it look like there is only one angle in your index >> file. >> >> Mark >> >> @ xaxis label "Degrees" >> @ yaxis label "" >> @TYPE xy >> @ subtitle "average angle: 9.87432\So\N" >> @with g0 >> @ world xmin -180 >> @ world xmax 180 >> @ world ymin 0 >> @ world ymax 0.0451172 >> @ xaxis tick major 60 >> @ xaxis tick minor 30 >> @ yaxis tick major 0.005 >> @ yaxis tick minor 0.0025 >> -180 0.015625 >> -179 0.011719 >> -178 0.015625 >> -177 0.000000 >> -176 0.035156 >> -175 0.031250 >> -174 0.019531 >> -173 0.019531 >> -172 0.023438 >> -171 0.015625 >> -170 0.015625 >> >> I did not include the distribution for rest of the angles. >> The second column is the fractional distribution of dihedrals >> with the corresponding angle in the 1st column. >> >> The distribution is averaged over time t = 800ps and 802 ps >> snapshots. I checked this part. >> >> Amit >> >> >> >> >> On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham >> <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au> >> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au>>> wrote: >> >> Amit Choubey wrote: >> >> Hi Mark, >> >> It does seem that the -all option averages the >> distributions. >> The thing is i was confused with "the first graph is the >> average, the rest are the individual angles." because when i >> tried it previously i only found 2 columns which were >> angle and >> distribution. >> >> But now i checked again explicitly by doing few more g_angle >> commands and it seems that -all does do what i wanted to >> do. I >> still dont know what the "rest are the individual angles" >> means. >> >> >> I haven't ever used it, but would have expected the output to be >> along the lines of >> >> Time "Average over all angles" Angle-1 Angle-2 ... >> 1 234 23 345 >> 2 123 234 232 >> 2 223 ... >> 3 323 >> >> What output do you get and what seems wrong to you? >> >> Mark >> >> On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham >> <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au> >> <mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> >> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au> >> <mailto:mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au>>>> wrote: >> >> Amit Choubey wrote: >> >> Hi everyone, >> >> I am trying to analyze dihedrals of molecules after a >> simulation. I am able to calculate dihedral >> distribution >> at ant >> particular time using g >> -angle and proper group using >> >> g_angle -f after_md.trr -b 800 -type dihedral -n >> chain1.ndx -od >> dihed12 >> >> This gives me the distribution at t=800 ps . What i >> really want >> is to see the dihedral distribution at all time steps >> (after 800 >> ps) in one go, and may be do some averaging later. >> Is there a >> straight forward way to do this. I can imagine >> that i could >> write a script file that could do this but then i >> dont >> want to >> deal with a lot of files, i rather want everything >> to be >> saved >> in a single file with multiple columns. Could someone >> suggest a >> trick for this? >> >> >> The first paragraph of g_angle -h suggests there's an >> option >> where >> "the first graph is the average, the rest are the >> individual >> angles." Does this work? >> >> >> Mark >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>>> >> >> >> http://lists.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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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