Question about the R_0 in the switching function for COORDINATION

[llga...@gmail.com]

Dear all,

I am new to PLUMED-2.1.3. When I read the tutorial about COORDINATION, I am confused about the R_0 parameter setting.

There is an example as following: COORDINATION GROUPA=1-10 GROUPB=20-100 R_0=0.3 NLIST NL_CUTOFF=0.5 NL_STRIDE=100

The explanation goes with this example is " For atoms 1-10 coordination numbers are calculated that count the number of atoms from the second group that are within 0.3 nm of the central atom."

In practice, the coordination number is calculated from a switching function, right? At R_0=0.3nm, the value of switching function seems around 0.5 (with default setting d0=0.0). So why it is "count the number of atoms from the second group that are within 0.3 nm of the central atom". In this explanation, it seems any distance go beyond this point, coordination number is treated as zero? But in fact, it shouldn't be so.

I am asking this because I am studying the -OH bond break with coordination calculation between O and H atom in -OH group. I have calculated the RDF for -OH group, which gives peak around 0.1 nm. It seems using the switching function with default d0=0.0 and a setting of R_0 around 0.11nm, s(r) goes to zero at r > 0.2 nm. Do we need to give some cutoff to make the coordination goes to zero (with D_MAX, STRETCH ?) ? Or some other suggestions?

Thanks a lot

Lili

[Gareth Tribello]

Hello

You are totally right about the switching function.  At r_0 the value is 0.5 and not zero and so strictly speaking the function is not counting the number of atoms from the second group that are within 0.3 nm.  The problem is that if we try and write what the switching function is actually calculating we end up with some very long and confusing sentences.  As a result we wrote something that is not strictly true but that gives you some idea of what is going on.  Eventually it is always clearer to look at what the mathematical functions are calculating.

Now as for your question what you can do is as follows.  Plot your RDF using gunplot.  You will have a peak for the first coordination sphere and another peak for your second coordination sphere.  You then plot the function that is being calculated by the switching function on the same axis.  If you are using a RATIONAL switching function you then have 4 parameters to play around with r0, d0, n and m.  You can adjust these so that your switching function is 1 at the first peak in the rdf and so that it decays to zero by the second peak.  Based on the information in your email you might set d0 to around 0.1 nm, r0 to 0.05 and n and m to 6 and 12.  These are a first guess though you should play around with these things yourself.  

As for D_MAX and STRETCH.  You should look at your final switching function and find at point at which it goes very small.  You can the corresponding distance value to be D_MAX and add the STRETCH keyword if you want.

I hope this helps

Gareth

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[llga...@gmail.com]

Thanks a lot, Gareth.

You cleared my doubt. And I tested my system with settings following your suggestion (You can adjust these so that your switching function is 1 at the first peak in the rdf and so that it decays to zero by the second peak). It seems working better.

Thanks a lot

Lili