Hai Sir ! Actually i want to see the dihedral angle (Cβ-S-S-Cβ) variation over time.I used the commands
"g_angle -f trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg -type dihedral -all" "g_chi -s gp123_full.gro -f gp123_full.trr -o order.xvg -jc Jcoupling.xvg -g chi.log -rama -all" Please suggest me the right options Thanks for ur concern 2009/4/1 Tsjerk Wassenaar <[email protected]> > Hi Venkat, > > What exactly do you mean with variations. Do you want to follow the > angle over time, or do you want distributions with mean and variance > estimates? g_angle and g_chi seem to be the appropriate tools. You > mention you tried all suitable options, but fail to explain what you > tried and what exactly it is you want. We need that sort of > information to be able to help you out. > > Cheers, > > Tsjerk > > 2009/4/1 Venkat Reddy <[email protected]>: > > First of all Thanks for ur reply ! > > I tried both g_angle and g_chi with all suitable options, but i didn't > get > > the required result.Can u plz help me in this regard ??? > > > > 2009/4/1 Antonia V. <[email protected]> > >> > >> Did you try g_angle?? > >> > >> Antonia > >> ________________________________ > >> Date: Wed, 1 Apr 2009 11:35:29 +0530 > >> From: [email protected] > >> To: [email protected] > >> Subject: [gmx-users] How to calculate the dihedral angle variations ??? > >> > >> Hi Everyone ! > >> How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide bridge) > >> dihedral angle during a simulation ????? > >> Thanks in advance > >> > >> > >> > >> Cheers from > >> Venkat Reddy Chirasani > >> M.Tech Bioinformatics > >> UNIVERSITY OF HYDERABAD > >> > >> ________________________________ > >> check out the rest of the Windows LiveT. More than mail-Windows LiveT > goes > >> way beyond your inbox. More than messages > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> 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 > > > > > > > > -- > > Venkat Reddy Chirasani > > M.Tech Bioinformatics > > UNIVERSITY OF HYDERABAD > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > gmx-users mailing list [email protected] > 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 > -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD
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