[gmx-users] How to calculate the dihedral angle variations ???

[Venkat Reddy]

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 <tsjerkw at gmail.com>

> 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 <venkat4bt at gmail.com>:
> > 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. <antonia_haha at hotmail.com>
> >>
> >> Did you try g_angle??
> >>
> >> Antonia
> >> ________________________________
> >> Date: Wed, 1 Apr 2009 11:35:29 +0530
> >> From: venkat4bt at gmail.com
> >> To: gmx-users at gromacs.org
> >> 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
> >>
> >> ________________________________
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> >
> >
> > --
> > Venkat Reddy Chirasani
> > M.Tech Bioinformatics
> > UNIVERSITY OF HYDERABAD
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
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-- 
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
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