Hi, all,
I am doing shell molecular dynamics and I have read the sw.itp. Now my
question is:
1. For the shell "atom", what element should be used in .pdb file, since the
77-78th digits of pdb file is element symbol ?
2. What does the 1 in [ polarization ] part mean in sw.itp?
3. Is it reasonable to set initial position of shell arbitrally and let energy
minimization to find the optimum position for shell?
I also do not understand [ exclusion ] part:
; iatom excluded from interaction with i
1 2 3 4 5
2 1 3 4 5
3 1 2 4 5
4 1 2 3 5
5 1 2 3 4
For the first line, does that mean that the interaction of 2, 3, 4 and 5 with 1
is excluded? If so, this table will exclude all the interactions. Is it right?
Thank you in advance.
Shuangxing Dai
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