Bond variations from the trajectory

Dear Lammps Users,

I have a molecular dynamics simulation done for a system
where part of the molecule undergoes elongation during the simulation
window and other remains same or decreased.

I would like to address this effect quantitatively to
bring out the possible reason of why this occurs.

For example, I can calculate the bond length for each structure
in the trajectory, through which possibly the standard deviation that provides
an estimate of the relative variations of the bond in the system.

But this is going to be a hard procedure.

Does any one have some ideas how this observation
can be well presented.
If so can you please share me your views.

Thanks in advance.
Vimala

there is no reason to post the (almost) same question twice.

Dear Lammps Users,

I have a molecular dynamics simulation done for a system
where part of the molecule undergoes elongation during the simulation
window and other remains same or decreased.

I would like to address this effect quantitatively to
bring out the possible reason of why this occurs.

For example, I can calculate the bond length for each structure
in the trajectory, through which possibly the standard deviation that
provides
an estimate of the relative variations of the bond in the system.

it is not quite clear what kind of transformation you are describing.
you can easily have an elongation of a molecule without changes in
bond length.

But this is going to be a hard procedure.
Does any one have some ideas how this observation
can be well presented.
If so can you please share me your views.

it is not easy to make any suggestions based on so little information.
parameters that might work are things like radius of gyration or
moments of inertia. depending on what kind of process you are looking
at, it may also be worth looking at a principal component analysis to
identify a preferred transformation "reaction coordinate".

axel.

You can also use the dump local command with compute bond/local
to output whatever bond lengths you like.

Steve