How can we access the information on the atom indexes involved in a given collective variable. I can see that it is possible to access this information in colvar and analysis classes. But is it possible to do the same in bias class?
Of course, you can define index and use them to define CV. However, the input still requires atom number to define the index. So you still have to know which atoms are included in the CV first.
According to Dr. Giovanni Bussi
"it is not, but you can access to the matrix of scalar product of gradients between two variables. This is done with geometric adaptive Gaussians.
You should:
define this function in your class:
bool checkNeedsGradients()const {return true;}
use getProjection(i,j) to access to this product.
Check generic/DumpProjections.cpp for an example
"
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