WALL, INTERVAL and INVERT keywords

[Rajeswari A.]

Dear Plumed users,

I find difficulties in understanding the following very related keywords. WALLS, INTERVAL and INVERT.

For example a CV of distance which i want to limit the space exploration between 2 to 5.

As far as i understand, walls is not allowing the system to explore beyond these limits by adding the wall potentials. Higher the Kappa value it is better blocking. Advice me if i am wrong.

What does the interval and invert keywords do when the distance is beyond the limit 2 and 5?  

INTERVAL CV 1 LOWER_LIMIT 2 UPPER LIMIT 5

INVERT CV 1 REFLECTION 1.6 INVERSION 6 MAXHEIGHT 4 LIMIT1 2 LIMIT2 5

When i use interval keyword alone (not included uwall and lwall) the system still sampling the distance beyond 5. What does it mean??? Should i always use interval keyword along with with UWALL and LWALL??? Then how would it be different from that of simply using only UWALL and LWALL alone??

Kindly help me to understand these three keywors - Walls, interval and invert.

Thank you,

Raji

[Alessandro Laio]

Dear Raji,
the WALL keyword simply adds an harmonic external potential to the system. It can be used to restrain the CV dynamics in a given range. The higher kappa, the more the system is blocked, but you have to be careful with the integrator (in MD too strong forces are not allowed)
The INTERVAL  (or, similarly, INVERT) keyword are used  in metadynamics in order to avoid the onset of systematic errors in regions where the derivative of the free energy is too high. For example,  the derivative of a coordination number CV diverges at zero, and metadynamics cannot compensate an infinite derivative. In these condition, one can use INTERVAL as follows:
INTERVAL CV 1 LOWER_LIMIT 0.1
This means that the forces from metadynamics are not considered for CV values below 0.1
 
Of course you can use WALL and INTERVAL together. For example, if a CV would naturally span the interval -infinity-infinity, but you want to reconstruct the free energy in a range, say 2-5, the correct syntax is

INTERVAL CV 1 LOWER_LIMIT 2 UPPER LIMIT 5

UWALL CV 1 LIMIT 5 KAPPA 3000.0
LWALL CV 1 LIMIT 2 KAPPA 3000.0

If you want to compute the free energy reliably  you have basically two alternatives: either you use well-tempered metadynamics (eventually with WALLS), or you use ordinary metadynamics with the INTERVAL (or INVERT)  keyword set appropriately (also, if necessary, with WALLS), and take the time-average of the history-dependent profiles (see, for example, http://people.sissa.it/~laio/Data/review-bemeta.pdf ).

Alessandro

--
You received this message because you are subscribed to the Google Groups "PLUMED users" group.
To view this discussion on the web visit https://groups.google.com/d/msg/plumed-users/-/B-NUJk6ATD0J.
To post to this group, send email to plumed...@googlegroups.com.
To unsubscribe from this group, send email to plumed-users...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/plumed-users?hl=en.

[Rajeswari A.]

Dear Alessandro,

Many thanks for your great help. I am now understand these keywords better. and of course the paper you linked is really useful. Thanks a lot.

Raji.