<div>Dear all,</div>
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<div>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:</div>
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<div>[ atoms ]</div>
<div>; nr type resnr resid atom cgnr charge mass</div>
<div>... .... .. ....... ........ ... .. .... .......</div>
<div>35 VS 1 DRG POT 6 0.03 0.0</div>
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<div>.... ..... ... . ...... .... ...... ... ...... .......</div>
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<div>[ virtual_sites3 ]</div>
<div>;site from funct theta d</div>
<div>35 32 33 34 3 90 0.5</div>
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<div>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?</div>
<div>2. How to use "COG" selection in my *.itp file?</div>
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<div>Thanks a lot!</div>
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