Problems encountered when running metadynamics using DISTANCE and ZANGLE as a collective variable

[William Hsu]

Dear all,

Recently I've been trying to run metadynamics using PLUMED on a very simple system, which is composed of a NaCl and a bunch of water molecules in the box. In the beginning, I used the original plumed.dat left by a former lab member to run the simulation and use the distance between Na+ and Cl- as the collective variable and I got a satisfactory result. The parameters in the plumed.dat are as follows:

Then, to get more realized about the meaning of parameters, I modified some of them as follows and run the simulation again:

Originally I thought that the meanings of GRID_MIN and GRID_MAX were used to set the minimum and maximum (i.e. the range) of the collective variable (distance) to be calculated. However, as I tried to plot the free energy surface against the distance, I found that the collective variable actually only ranged from 0 to 3. Also, I was not sure if the meaning of GRID_BIN was the number of data points of the specified CV (In the user guide, it was described as the number of bins for the grid, but actually I was not sure about the meaning of a grid or bin). Therefore, what I modified were only the values of GRID_MIN, GRID_MAX and GRID_BIN. However, I later encountered  an error as follows:

I couldn't the error understand very well. I think that I might misunderstand the meanings of GRID_MIN, GRID_MAX or GRID_BIN and my determination of these parameters might cause the simulation to be infeasible. Therefore, I'm wondering if anyone has any idea about what was going on? Also, Could you please give me some guidelines when deciding the appropriate values of these three parameters? In addition, I also tried to take the angle between the z-axis and vector connecting Na+ and Cl- using ZANGLE. However, I was not sure about whether the unit of angle would be rad or degree. Therefore, I set the parameters as follows:

And then I encountered the error as follows:

It was shown that the parameters could not be read correctly at the very beginning, but I didn't know the reason for that.
Could anyone give me some suggestion?

Any comments or experience shared will be highly appreciated!
Thank you all in advance.Wei-Tse