Shuangxing Dai wrote:
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 ?
Anything you like. Gromacs does not use this information anyway.
2. What does the 1 in [ polarization ] part mean in sw.itp?
Function type, see manual ch. 5.
3. Is it reasonable to set initial position of shell arbitrally and let
energy minimization to find the optimum position for shell?
At first step the shell will be put in the place of the virtual site and
will be minimized from there.
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?
Yes. You need at least two molecules to do anything useful.
Thank you in advance.
Shuangxing Dai
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