Thanks to Steve, Rutuparna and Wan Liang for your suggestions last time.
Here are some new observations.
1. The problem with the drop in temperature went when I removed the fix angular
momentum command that was acting on the group silver (silver is the cluster at
the centre). I observed things were going wrong only after the newly introduced
copper atoms were hitting the silver cluster. But this fix momentum was doing
fine when there was only silver or copper atoms were far away from silver.
This triggers I question: is there something wrong with this fix momentum
2. Now I removed the fix silver momentum angular command. All thermodynamic
parameters I am calculating now are on the 'all' group. So when I introduce a
copper atom into the system (ref. input file below), I expect the total energy
to go up. But this is not happening. The total energy remains constant. The
change that happen are: the temp (and thus ke) rises and the pe decreases every
time a copper atom hits the silver core. Why does this happen?
I assign newly created copper atoms to group copper everytime a new copper atom
is created. Then won't they automatically get assigned to group 'all'?
3. The last part of rdf output file reads:
r, g(2,1,r), ncoord(2,1,r)
0.027750 0.000000 0.000000
5.522250 1034.970646 1916.933333
What does this ncoord calculate? The total no. of neighbours of type 1 within
the cut-off an atom of type 2?
Could you please throw some light on these. I am giving my current input file
here for your reference.