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Re: [lammps-users] Histogram of Dihedral Values
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Re: [lammps-users] Histogram of Dihedral Values


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 24 Oct 2017 12:00:23 -0400

On Tue, Oct 24, 2017 at 11:22 AM, Charles Belina
<charles.belina@...7193...> wrote:
> Hey everyone,
>
> I’m attempting to obtain a histogram of dihedral values. Since I only care about the value of a certain dihedral, I defined a group and then used a compute command:
>
> group DiHe type 2 3 4 5 6 7 8 9
> compute 1 DiHe dihedral/local phi
>
> To get the histogram, I used:
>
> fix DiHeCalc DiHe ave/histo 1000 9 1 0 360 180 c_1 file DiHe.histo
>
> The simulation run time is only 20 ps (this is just a test run), and as far as I understand, this fix command should run the aforementioned compute command over the group 9 times, with the interval between measurements being 1000 time steps (1 ps). There are 180 histogram bins, each with a size of 2 degrees, starting at 0 and ending at 360. Upon running the simulation, however, the DiHe.histo file is created but is entirely empty. I received the following error in my output file:
>
> ERROR: Illegal fix ave/histo command
>
> I thought that I might have defined my group incorrectly, so I later ran the fix over all atoms and nevertheless received the same error. Can someone help me out please? If you needed to obtain the histogrammed values for a certain dihedral, would you even approach the problem this way? Any advice would be greatly appreciated,

there are two problems:
- your Nevery, Nrepeat, Nfreq is invalid. it probably should be 1000 9
9000, please re-read the docs and study the examples given carefully.
- your compute returns a "local vector" not a scalar, so you need to
use "mode vector"

axel.


>
> Charles Belina
> Student Researcher
> Skolkovo Institute of Science and Technology
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.