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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