Good morning to everyone,
To simulate the binding of an organic molecule to Zr4+ ion I am using the
12-6-4 LJ potential (on Amber20).
I think that the c4 parameter is actually taken into account during the
simulation, indeed in the section Potential Function of the output file of
pmemd.cuda there is the flag "lj1264 = 1".
However, when I load the topology file in cpptraj I get the following
mistake:
"Warning: Amber topology flag 'LENNARD_JONES_CCOEF' is unrecognized and
will be skipped" .
Can someone help me with this?
I also have another question: is there a way to print the c4/r^4 energy
component between two atoms along the simulation?
I tried to search an action of cpptraj doing so, the pairwise action
evaluates the vdw energy between group of atoms, but not the single
components.
best,
Giulia
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Received on Thu Aug 04 2022 - 13:33:46 PDT
