boundary s s s | non-periodic dimension

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1

From our simulations using non-periodic dimension, we observed

simulation results were quite different depending on the starting
coordinates dimension. Our aim was to fold the stretched peptide into
folded structure.

[case 1] Initial x, y, z-coordinates min/max, i.e. system dimension,
is all wide for x, y, z-dimension in lammps.data file
-3.3994429 40.641 xlo xhi x-dim: 44.0404429
-1.6777038 26.052 ylo yhi y-dim: 27.7297038
-52.796 1.6692155 zlo zhi z-dim: 54.4652155

[case2] Same stretched structure as in case 1, but has different
origin thus narrow z-dimension in lammps.data file
2.496995 65.1194942 xlo xhi x-dim: 67.6164892
0.839991 40.7689475 ylo yhi y-dim: 41.6089385
-2.13122 2.1312148 zlo zhi z-dim: 4.2624348 ****

The z-dimension in [case2] is confined in a restricted
extent; In fact we expect this initial dimension information is
adjusted by LAMMPS during simulation, however for the given the same
simulation time [case1] folded into globular shape quickly, whereas
[case2] didn't fold at all and yet stretched.
Is it possible that "boundary s s s" might prevent a drastic
dimension change thus be stuck in a limited dimension?

Thanks for your help in advance.

2

>From our simulations using non-periodic dimension, we observed
simulation results were quite different depending on the starting
coordinates dimension. Our aim was to fold the stretched peptide into
folded structure.

this is a very vague description of the system that you are
simulating. thus it is near impossible to comment on the outcome.

[case 1] Initial x, y, z-coordinates min/max, i.e. system dimension,
is all wide for x, y, z-dimension in lammps.data file
-3.3994429 40.641 xlo xhi x-dim: 44.0404429
-1.6777038 26.052 ylo yhi y-dim: 27.7297038
-52.796 1.6692155 zlo zhi z-dim: 54.4652155

[case2] Same stretched structure as in case 1, but has different
origin thus narrow z-dimension in lammps.data file
2.496995 65.1194942 xlo xhi x-dim: 67.6164892
0.839991 40.7689475 ylo yhi y-dim: 41.6089385
-2.13122 2.1312148 zlo zhi z-dim: 4.2624348 ****

The z-dimension in [case2] is confined in a restricted
extent; In fact we expect this initial dimension information is

what does that mean?

adjusted by LAMMPS during simulation, however for the given the same
simulation time [case1] folded into globular shape quickly, whereas
[case2] didn't fold at all and yet stretched.

there are a large number of factors that can explain
the difference you are seeing, but without more details
about your simulation, e.g. is there solvent involved?
what kind of force field? how is the initial configuration
generated? what is the difference between the two
initial configurations, if any?

Is it possible that "boundary s s s" might prevent a drastic
dimension change thus be stuck in a limited dimension?

nope. when using s s s with different cell dimensions, but
otherwise identical input decks, the only potential difference
is a different distribution of the processors in the domain
decomposition for parallelization. that may have some small
impact on forces due to truncation errors, but that is
well withing the error margins of the simulation overall.

if you want more specific advice, you have to provide
more specific information. answers in general can only
be as good as the question. :wink:

cheers,
    axel.