setting the value of qmLinkElement in NAMD/QMMM script

From: jing liang (
Date: Thu Dec 02 2021 - 03:23:24 CST


I don't understand well the description of the parameter qmLinkElement from
the documentation page:

It looks to me that when there are two or more bonds I need to pass the
atom numbers of the MM atoms involved. Are these atom numbers obtained from
the *psf file?

I used QwikMD for setting the simulation and when I look at the value that
this parameter got it says:

#QMLinkElement "18 38 Cl"

but the numbers 18 and 38 don't correspond to the atom numbers in the psf
file of the atoms involved in the bond.

I wonder how the numbers 18 and 38 are obtained? What they are?

thank you

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST