[gmx-users] g_angle command output

[David van der Spoel]

On Fri, 2005-10-21 at 14:26 +0200, Ester Chiessi wrote:
> Thanks for your answer.
> 
> I realized that the Time between transitions: 116.601 ps is calculated as:
> total trajectory time/(#transitions per dihedral)
> 
> total time=1100 ps
> total #transitions=11133
> total #dihe=1180
> 1100*1180/11133=116.6 ps
> 
> Now, I was considering the trhisto.xvg output.
> 
> I interpret the data y(x) as number of dihedral angles (y) showing a 
> particular average time between transition (x), where x = totaltime 
> (1100ps)/(#trans of that dihedral +1).
> I though this analysis was performed for each dihedral of the index file, so 
> I espected a sum of all the y values in the trhisto equal to 1180 ( the 
> total #dihe).
> I found a sum of 881.
> Have you any comment?
> 
> I tried to evaluate an average conformation lifetime <t> as follows:
> >From (x,y) values in trhisto:
> <t>=( sum of x*y )/881
> that corresponds to an average of the abscissa values, weighted for the 
> dihedral fraction y/881.
> I obtained <t>=218.48 ps.
> 
> Do you think this value is meaningful?
> 
I'm sorry but it was a while ago since this code was written, I'm not
even sure that I wrote it... Please check the source code in
src/tools/gmx_angle.c


> Thanks again
> Ester
> 
> 
> 
> 
> 
> 
> 
> ----- Original Message ----- 
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Thursday, October 20, 2005 1:46 PM
> Subject: Re: [gmx-users] g_angle command output
> 
> 
> > On Thu, 2005-10-20 at 12:14 +0200, Ester Chiessi wrote:
> >> Hi
> >>
> >> I was performing an analysis of the conformational dynamics of my system 
> >> ( a
> >> polymer network in SPC water ) by g_angle ... -type dihedral .....
> >> Using the options -ot and -oh  I red in the output of the command:
> >> ........
> >> Time between transitions: 116.601 ps.
> >>
> >> What does exactly represent this value?
> >
> > I think it just counts the number of transitions and divides the total
> > time by that number.
> >>
> >> >From the dihedral histogram I estimated an average conformation lifetime 
> >> >of
> >> 218 ps.
> > How did you do that?
> >
> >>
> >> Thanks for your attention
> >> Ester
> >>
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> > -- 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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