Dear lammps-users,
I have a question regarding the steered md (using fix smd).
I have a surface and I want to pull off a moiety from it by constant velocity.
I used fix smd as below:
group pull id 409
group surf molecule 1
fix 1 all nvt temp 298.15 298.15 100.0
fix 2 surf smd cvel 1.0 0.0005 couple pull NULL NULL 27.0 14.0 (I want to move the atom 409 up, towards the point 0 0 27, at this point the distance btw center of mass of the surface and atom 409 is about 14.0 Ang and that is what I have set for the R0)
When I run this, atom 409 comes off of the surface but as soon as it gets the distance of ~3A from the surface, it suddenly jumps up (to 0 0 27)
It seems to me that a constant force is applied and when the attraction btw surface and atom 409 is small, it pulls the 409 to the middle of the box
Then what happens to the constant velocity which I thought I would have by cvel…
I appreciate any clarification on this issue
Thanks
Dear lammps-users,
I have a question regarding the steered md (using fix smd).
I have a surface and I want to pull off a moiety from it by constant
velocity.
I used fix smd as below:
group pull id 409
group surf molecule 1
fix 1 all nvt temp 298.15 298.15 100.0
fix 2 surf smd cvel 1.0 0.0005 couple pull NULL NULL
27.0 14.0 (I want to move the atom 409 up, towards the point 0 0 27, at this
point the distance btw center of mass of the surface and atom 409 is about
14.0 Ang and that is what I have set for the R0)
When I run this, atom 409 comes off of the surface but as soon as it gets
the distance of ~3A from the surface, it suddenly jumps up (to 0 0 27)
It seems to me that a constant force is applied and when the attraction btw
surface and atom 409 is small, it pulls the 409 to the middle of the box
Then what happens to the constant velocity which I thought I would have by
cvel....
it is difficult to follow from that description. but
i am certain that you want to have R0 at 0.0
R0 is not the R0 that people usually expect.
i am about to clean up fix smd and that option
will go and be replaced with a different flag
that allows to define an initial distance (which
is currently picked fully automatically).
axel.