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Re: [lammps-users] determination of structure after NPT run
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Re: [lammps-users] determination of structure after NPT run


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 6 Jul 2017 10:24:45 -0400

...or use one of those RMSD fit and alignment tools that people in
biosimulations use to determine how much (and where) their protein
structure has changed.

axel.

On Thu, Jul 6, 2017 at 10:20 AM, Steve Plimpton <sjplimp@...24...> wrote:
> There are several computes which look at the local
> neighbors of each atom and calculate quantities
> related to crystal structure.  E.g. compute coord/atom,
> compute centro/atom, compute cna/atom.
>
> Steve
>
> On Wed, Jul 5, 2017 at 10:52 PM, abrar Quadery via lammps-users
> <lammps-users@lists.sourceforge.net> wrote:
>>
>> Dear LAMMPS users,
>> how can one verify after a NPT run that quartz remained as quartz (quartz
>> is a generic here). Maybe this is same as asking how one can determine the
>> crystal structure from a given set of atomic coordinates. A snapshot from a
>> MD dynamics will record the displacements due to thermal vibrations, how
>> that will be taken care of while determining the structure? I know this is
>> not exactly a lammps question, but I couldn't find the answer elsewhere. My
>> apology for that.
>>
>>
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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.