Hi,
I’m simulating a polymer and the bond length should be 1.2 nm.
I made a mistake and I didn’t considered that in the LJ unit system, length would be dimensionless by (distance)/6.25. So if the bond length in my data file is 1.2 it would be actully 1.2*6.25 ~ 7nm right?
Is there any way to change the LJ unit of length from 6.25(L J) to 1 ?
Or just reduce my bond lengths through my code?
thanks
Hi,
I'm simulating a polymer and the bond length should be 1.2 nm.
I made a mistake and I didn't considered that in the LJ unit system, length
would be dimensionless by (distance)/6.25. So if the bond length in my data
file is 1.2 it would be actully 1.2*6.25 ~ 7nm right?
where does this factor 6.25 come from?
it is not clear why you talk about nm and then reduced units.
you are obviously making the extremely optimistic assumption that
people on the list here have seen your input file or are able to read
your mind.
Is there any way to change the LJ unit of length from 6.25(L J) to 1 ?
Or just reduce my bond lengths through my code?
the simplest solution is to rebuild the data file. i assume you use
some tool/program for it, so it should not be much effort to redo this
step.
next option would be to change your bond parameters and run a
minimization, but with an incorrect initial geometry, your system will
be a mess, so i don't know what that would achieve.
again, your description is vague and confusing, as there is no
explicit bond length in a data file outside of the bond coefficients,
and those are extremely easily changed, either with a text editor or
through overriding them in the input file with the bond_coeff command.
in the future, please make a better effort to describe your effort and
provide sufficient information. if people will have to mostly guess
what is going on, you're not going to make friends and your chances of
getting accurate help or any help at all will dwindle.
axel.