Dear All,

I want to pull a I atom out of a surface using steered MD simulation. The initial position of I atom along the pulling direction (z axis) is 73.0, and the commands for SMD is:

group I id 1676

group rest subtract all I

velocity rest zero linear

fix mom rest momentum 1 linear 1 1 1

variable K equal 3000

variable vel equal -0.00001

variable z equal 95.0

fix pull I smd cvel K {vel} tether NULL NULL $z 0.0

variable F equal f_pull[4]

variable r0 equal f_pull[5]

variable r equal f_pull[6]

variable PMF equal f_pull[7]

fix PMF all print 1000 “{F} {r0} {r} {PMF}” file PMF.profile

fix npt rest npt temp $T $T 100 x 1 1 500 y 1 1 500

run 2000000

In PMF output file, however, the value of F and PMF are extremely large. And r0 is not equal to r. In addition, I also check the motion of such I atom, and it doesn’t move.

I cannot find any possible reason for such problem. Hope you can give me some comments and suggestions.

Best,

MC

Dear All,

I want to pull a I atom out of a surface using steered MD simulation. The

initial position of I atom along the pulling direction (z axis) is 73.0,

and the commands for SMD is:

group I id 1676

group rest subtract all I

velocity rest zero linear

fix mom rest momentum 1 linear 1 1 1

variable K equal 3000

variable vel equal -0.00001

variable z equal 95.0

fix pull I smd cvel K {vel} tether NULL NULL $z 0.0

variable F equal f_pull[4]

variable r0 equal f_pull[5]

variable r equal f_pull[6]

variable PMF equal f_pull[7]

fix PMF all print 1000 "\{F\} {r0} \{r\} {PMF}" file PMF.profile

fix npt rest npt temp $T $T 100 x 1 1 500 y 1 1 500

run 2000000

In PMF output file, however, the value of F and PMF are extremely large.

And r0 is not equal to r. In addition, I also check the motion of such I

atom, and it doesn't move.

I cannot find any possible reason for such problem. Hope you can give me

some comments and suggestions.

the way fix smd is implemented (as an adapted version of fix spring), you

don't want to pull toward a point but rather away from a point.

thus try the following and change the sign of the velocity:

fix pull I smd cvel K {vel} tether NULL NULL $(xcm(pull,z)) 0.0

also, your velocity seems rather small.

why don't you try a simple system with fix nve and just two atoms (one of

which kept immobile) for testing what are the right settings for fix smd

are?

... and finally, the usual complaints:

- you don't say which version of LAMMPS and on what platform you are using

- your input is incomplete, thus you force people to guess

axel.