[lammps-users] fix smd/WHAM/PMF

Dear Lammps users:

I am trying to calculate the PMF of a Na+ above the crystal layer. But I am confused about the command “fix smd”, I don’t understand exactly “the equilibrium distance of the spring” and “accumulated PMF (the sum of pulling forces times displacement)” mean. Isn’t that “the equilibrium distance of the spring” equal to R0 ? And “accumulated PMF” is the final value “potential of mean force” ?

And can I use “umbrella sampling” in lammps directly or need other software ?

Thanks a lot

Shen

Dear Lammps users:

I am trying to calculate the PMF of a Na+ above the crystal layer. But I am confused about the command “fix smd”, I don’t understand exactly “the equilibrium distance of the spring” and “accumulated PMF (the sum of pulling forces times displacement)” mean.

Isn’t that “the equilibrium distance of the spring” equal to R0 ?

no. R0 is a term that fix smd has inherited from fix spring. it should be set to 0.0 for almost any use case.

And “accumulated PMF” is the final value “potential of mean force” ?

And can I use “umbrella sampling” in lammps directly or need other software ?

it should be possible with fix spring.

in general for these kind of applications I would recommend to use either the fix colvars from the USER-COLVARS package or fix plumed from the USER-PLUMED package. both fixes are part of packages that have a detailed and good documentation outside of LAMMPS, tutorials and are compatible with multiple MD packages and are in many ways far more sophisticated and flexible than what fix smd and fix spring offer.

Axel.

Dear Lammps users:

Thanks for your reply!

But I still don’t understand the 6th column “the distance between the two reference points” when I use the keyword “tether”, as it just has the only group, so what “the two reference points” refers?

And when I set “fix 4 na smd cvel 23.9006 -1.0e-6 tether NULL NULL 7.60106 0.0”, why I still get value in the 4th column and 5th column(Force_x and Force_y), the manual write “For both the tether and couple styles, any of the x,y,z values can be specified as NULL which means do not include that dimension in the distance calculation or force application”?

Attach my in-file

Shen Peng

MMT_PMF.in (2.16 KB)

Dear Lammps users:

Thanks for your reply!

But I still don’t understand the 6th column “the distance between the two reference points” when I use the keyword “tether”, as it just has the only group, so what “the two reference points” refers?

in couple mode the second reference point is the tether coordinate that you specify in the command.

And when I set “fix 4 na smd cvel 23.9006 -1.0e-6 tether NULL NULL 7.60106 0.0”, why I still get value in the 4th column and 5th column(Force_x and Force_y), the manual write “For both the tether and couple styles, any of the x,y,z values can be specified as NULL which means do not include that dimension in the distance calculation or force application”?

the documentation says:

The quantities in the vector are in this order: the x-, y-, and z-component of the pulling force, the total force in direction of the pull, the equilibrium distance of the spring, the distance between the two reference points, and finally the accumulated PMF (the sum of pulling forces times displacement).

Thus the x component of the force is in column 1 and the y component in column 2 and NOT in columns 4 and 5, respectively.