[gmx-users] g_angle command output

Ester Chiessi ester.chiessi at uniroma2.it
Fri Oct 21 14:26:11 CEST 2005

```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?

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?
>
>>
>> Ester
>>
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
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