[gmx-users] Calculation of the components of (ionic) current using g_current

Andrew DeYoung adeyoung at andrew.cmu.edu
Mon May 7 19:00:23 CEST 2012


g_current calculates the (ionic) current in the output file specified by the
-o switch (by default, "current.xvg").  Specifically, each component (x, y,
and z) of the current is computed and printed.

My question is, is the current that is computed the current of atoms (which
each have partial charges), or is it the current of molecules (ionic
molecules have non-zero charge, whereas neutral molecules have zero charge)?
I am guessing that it is the former -- the current of atoms.  However, I am
not certain, because when I run g_current, part of the output says, for

"Split group of 6144 atoms into 512 molecules"

which seems to imply that the code uses the topology (I provide the code
with a .tpr file) to determine the connectivity of atoms.

Thanks so much!

Andrew DeYoung
Carnegie Mellon University

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