I am trying to calculate the potential of mean force between two groups of particles, each group belongs to a larger molecule (for example, several beads in a bead-spring polymer chain).
But I found there are two methods for calculating potential of mean force,
one is fix smd, the other one is fix colvars.
Could you tell me which one is closer to the tutorial?
I have made some tests using fix smd,
but still can’t figure out something,
I think I should use tether option combined with fix spring/self if I would like to fix the position of one group and move the other group along x,y or z direction.
But should I set a fix position (x,y,z) for tether values? I mean whether it’s the final position for the moving group.
I am trying to calculate the potential of mean force between two groups of
particles, each group belongs to a larger molecule (for example, several
beads in a bead-spring polymer chain).
But I found there are two methods for calculating potential of mean force,
one is fix smd, the other one is fix colvars.
Could you tell me which one is closer to the tutorial?
they are the same. however, in the tutorial it is very clearly explained,
that the "pull code" (i.e. fix smd or the smd option of colvars) are *not*
the method used to compute the PMF, but simply the method used to generate
initial coordinates for the umbrella sampling. steered MD (or SMD) is one
of many alternative methods to compute a PMF (fix colvars specializes in
this).
to do the umbrella sampling itself, you need to do multiple runs with
either fix spring or fix colvars.
I have made some tests using fix smd,
but still can't figure out something,
I think I should use tether option combined with fix spring/self if I
would like to fix the position of one group and move the other group along
x,y or z direction.
But should I set a fix position (x,y,z) for tether values? I mean whether
it's the final position for the moving group.
neither. from what the tutorial says, you should not fix anything in
space, but rather use the biasing (fix spring or colvars) to keep the two
groups at the predefined distance for the umbrella sampling bin.
overall, it looks a lot like you are trying to do the tutorial without
having studied the underlying theory sufficiently well. i suggest you leave
the computer and simulations alone for a bit and catch up on that. this
will allow you to do better informed choices in the future and avoid
mistakes (and there are several pitfalls) from following a tutorial
"blindly" without knowing what you are doing.