I want to do umbrella sampling for different coordination of amino acid through different distances (in Z dimension) from nanotube. The nanotube axis is along X axis. The COM of nanotube is in Z=1.5 and its outer curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15 (because the nanotube radius is 0.65nm). The initial distance of amino acid from nanotube is 2nm. The question is how should i choose the least box size(specially in Z dimension) that some artifacts (because of PBC in all dimensions) doesn’t happen?
Would you please help me?
Regards,
-Rose
I want to do umbrella sampling for different coordination of amino acid
through different distances (in Z dimension) from nanotube. The nanotube
axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
(because the nanotube radius is 0.65nm). The initial distance of amino acid
from nanotube is 2nm. The question is how should i choose the least box
size(specially in Z dimension) that some artifacts (because of PBC in all
dimensions) doesn't happen?
please note, that what you are asking about is a question about how to do
your research and *not* about how to use LAMMPS (you would need to ask the
same question if you would be using any other MD simulation software). and
thus this is something that you should rather discussion with your
adviser/supervisor/tutor. apart from that, if you look at what you are
asking and how you are asking it, it should be straightforward to construct
some simple tests to check for yourself, how large the impact from periodic
boundaries is, and you can from that estimate, how large you have to make
your box to reduce the impact from periodicity until it is lower than the
threshold you desire.
axel.