[lammps-users] fix smd

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1

Dear lammps researchers,

I want to calculate the PMF(free energy) of a gas molecule passing through the solution/vacuum interface using ‘fix smd’ command as (z direction considerd only):

fix 3 gas smd cvel K v tether NULL NULL z 0.0

How to determine the spring constant(K), the velocity of pulling(v) and the tether point(z), is there any menthods or suggestions? Besides, as the manual explains the last two output quantitie are the distance between the two reference points, and finally the accumulated PMF. Does the ‘distance between the two reference points’ stands for the distance between the tether point(if Ro=0) and the center of mass of group ‘gas’ ? Does the last ‘accumulated PMF’ is the PMF of the gas molecule along the passing coordinates ? Why it’s a ‘accumulated’ values?

Thank you very much in advance.

2

First off, please note that fix smd is very old and effectively unmaintained. We primarily keep it in the LAMMPS distribution because of its simplicity and usefulness beyond computing free energies via steered MD.

The same functionality (plus a lot more) is also available in either the COLVARS or the PLUMED package which in addition offer many, many more features to compute and analyze free energy profiles. Those two packages have extensive documentation and examples and tutorials.

As for your question about the parameters and what is meant by “accumulated” potential of mean force, I suggest you read the associated publications describing the methodology. Then it should become self-explanatory. There also is a textbook worth looking at: https://link.springer.com/book/10.1007/978-3-540-38448-9