Dear LAMMPS user :
I want to run SMD. in this case, I intend to pull an amino acid in a path in Z direction. But a paragraph of manual was confusing for me :
“The tether style attaches a spring between a point at a distance of R0 away from a fixed point x,y,z and the center of mass of the fix group of atoms. A restoring force of magnitude K (R − R0) Mi / M is applied to each atom in the group where K is the spring constant, Mi is the mass of the atom, and M is the total mass of all atoms in the group. Note that K thus represents the total force on the group of atoms,not a per−atom force.
In cvel mode the distance R is incremented or decremented monotonously according to the pulling (or pushing) velocity”
what is mean R0 and R and fixed point? is it as follows?
[group]-----////-----[]--------------[fixed point]
<----R0---->
<--------------R ------------->
spring : -----////-----
distance R0 : --------------
if it be as above, How can increase distance R monotonously?I think While the fixed point moves, the group is also follows it and distance R shouldn’t increase monotonously. I think according to this site :
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node17.html
distance R should be little changed.
please clarify this issue for me…
Thanks for advance.
Farrokh
Dear LAMMPS user :
I want to run SMD. in this case, I intend to pull an amino acid in a path in
Z direction. But a paragraph of manual was confusing for me :
"The tether style attaches a spring between a point at a distance of R0 away
from a fixed point x,y,z and the center of mass of the fix group of atoms. A
restoring force of magnitude K (R - R0) Mi / M is applied to each atom in
the group where K is the spring constant, Mi is the mass of the atom, and M
is the total mass of all atoms in the group. Note that K thus represents the
total force on the group of atoms,not a per-atom force.
In cvel mode the distance R is incremented or decremented monotonously
according to the pulling (or pushing) velocity"
what is mean R0 and R and fixed point? is it as follows?
[group]-----/\/\/\/\-----[]--------------[fixed point]
<----R0---->
<--------------R ------------->
spring : -----/\/\/\/\-----
distance R0 : --------------
no. it is:
<--/\/\/\/\-><------R-------><----R0--->[fixed point]
if it be as above, How can increase distance R monotonously?I think While
the fixed point moves, the group is also follows it and distance R shouldn't
increase monotonously. I think according to this site :
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node17.html
distance R should be little changed.
please clarify this issue for me..
just disregard R0 and set it to 0.0. R0 was left in the smd code because
it is derived from fix spring. however, it turns out that it causes
more confusion
than good. thus my recommendation is to set it to 0.0 and forget about R0.
cheers,
axel.
Dear Axel,
Thanks for your reply.
Ok. so, for R0=0 we have :
[group]<–////–><------R------->[fixed point]
I have still some questions :
-
is the" fixed point(x,y,z)" equivalent to the"tether point"? meaning :
[group]<–////–><------R------->[fixed point=tether point]
-
does " fixed point(x,y,z)" move to the right with constant velocity? meaning :
[group]<–////–><------R------->[fixed point]
[fixed point] --> v
-
for example, an amino acid (group) places in the initial in ( 0,0,12) and we want to pull it on straight line to (0,0,30), then what should be (x,y,z) values in fixed point? Does it represent direction of move only?
Thanks for your attentions,
Farrokh
Dear Axel,
Thanks for your reply.
Ok. so, for R0=0 we have :
[group]<--/\/\/\/\--><------R------->[fixed point]
I have still some questions :
1) is the" fixed point(x,y,z)" equivalent to the"tether point"? meaning :
[group]<--/\/\/\/\--><------R------->[fixed point=tether point]
fix smd in tether mode is equivalent to fix spring in tether mode
if you run with constant velocity 0.0.
2) does " fixed point(x,y,z)" move to the right with constant velocity?
meaning :
[group]<--/\/\/\/\--><------R------->[fixed point]
[fixed point] --> v
well, you can see it as you like. technically the value of R gets
changed, but that is equivalent to moving the point. please note
that R is allowed to become negative and the pulling will continue.
3) for example, an amino acid (group) places _in the initial_ in ( 0,0,12)
and we want to pull it on straight line to (0,0,30), then what should be
(x,y,z) values in fixed point? Does it represent direction of move only?
you can pick any point (0,0,N) with N > 12
if you want to stop at (0,0,30) you have to compute
as to how many MD steps at the given pulling
velocity this amounts to and then stop the MD.
axel.