[gmx-users] how to use virtual sites?

[Chuipeng Kong]

Dear all,

I know there are sections about virtual sites usage in gromacs manual. But
it is somehow unclear for me to use. So I would like to ask how to use
virtual sites in my input file. I have follow the the example from
"tip4p.itp" and write my own virtual site is *.itp as:

[ atoms ]
; nr   type  resnr resid  atom  cgnr    charge     mass
...     ....   ..   .......       ........   ...  .. ....  .......
35    VS   1   DRG      POT   6   0.03    0.0

....   .....   ...  . ...... ....   ......  ...  ......   .......

[ virtual_sites3 ]
;site  from                                   funct     theta     d
35        32            33          34           3          90    0.5

1. I also define the "VS" in "atomtypes.atp"  and "ffnonbonded.itp", Do I
still need to give the corresponding coordinates for "VS" in *.gro file?
2. How to use "COG" selection in my *.itp file?

Thanks a lot!
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