Calculate SMD PMF
Description
This function calculates the potential mean force (PMF) based on the results of a steered molecular dynamics (SMD) run. It computes both the general functions PMF(z) and the specific integral to determine the DeltaG of the well/barrier. This post-processing step must be performed after an MD simulation in which the SMD dynamics is performed, meaning a node that returns the forces and position during a pulling process.
Latest version
Allowed number of parents: 1
| Parameter | Description | Value type | Value restrictions | Default value | Units |
|---|---|---|---|---|---|
PMF mode |
The mode to calculate the PMF: Either |
selector |
well, barrier |
well |
N/A |
Running average filter length |
The filter length (in ps) to calculate the running average of the raw data |
float |
>0 |
0.0 |
ps |
Running average stride |
The stride (in ps) to calculate the running average of the raw data (i.e. only every n-th data point will be calculated, n = stride in ps) |
float |
>0 |
0.0 |
ps |
Kernel for running average |
Indicate the kernel used to calculate the running average. The average is calculated as a convolution with this kernel. |
selector |
uniform, gaussian |
uniform |
N/A |
Sigma of Gaussian |
Indicate the sigma of the Gaussian used as kernel (only for kernel = Gaussian) |
float |
>0 |
1000 |
ps |
Spacing to calculate the PMF function |
Indicate the grid spacing for the calculation of the PMF function (in nm) |
float |
>0 |
0.0 |
Angstrom |
Lower integration bound |
The lower integration bound for the integration of the PMF (i.e. a position at “infinity” where the forces are zero) |
float |
any float |
0.0 |
Angstrom |