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Re: [lammps-users] Using a Group Command to Specify a Certain Dihedral Calculation
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Re: [lammps-users] Using a Group Command to Specify a Certain Dihedral Calculation


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 1 Nov 2017 11:21:02 -0400

On Wed, Nov 1, 2017 at 9:57 AM, Charles Belina
<charles.belina@...7193...> wrote:
> Hey Axel, thanks so much for the tips! They helped me solve the previous
> problem, but now I've encountered a new, related one. After obtaining some
> unexpected peaks when I plotted the dihedral histogram, my professor and I
> realized that they were occurring because my group command was too
> encompassing:
>
> group DiHe type 3 6 7 8
> compute 1 DiHe dihedral/local phi
>
> Whereas I had only wanted the compute command to compute the value of one
> dihedral per monomer, it had computed others as well because there were
> multiple atoms of these types in each monomer. It seems that defining a
> group with types is not specific enough in my case, but with such a big
> system (6400 atoms), using atomic ID's does not seem realistic either. Maybe
> there is a way to restrict the compute to the case where all four atoms are
> bonded? What do you think is the best way to solve this problem?

the compute *is* already restricted to only consider explicitly
defined dihedrals.

if you say you have many monomers and you want to look at only
specific atoms in them, then i would assume, that your atom ids should
follow a pattern where the individual atom id is like the atom id in
the first monomer plus the molecule/monomer id times the number of
atoms per monomer. for that you can define patters, or in more complex
cases, use an atom style variable (value != 0 => atom is included in
group; value == 0 => atom is not included).

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.