GROMACS version:5.1.40
GROMACS modification: Yes/No
Hi, I was trying to use [virtual_sites_2] to see the halogen bond between MeOH_O and EP1 and EP2 of C-Cl bonds in dichloromethane. But after production run I find the interaction energies between them straight 0. I used small positive charges on EP1 and EP2( +0.003). No error occured otherwise.
I included two virtual sites in Ch2Cl2.itp as:
[ atoms ]
6 EP 1 DCM EP1 1 0.0300 0.0000 ; sigma-hole site on Cl0 (mass 0)
7 EP 1 DCM EP2 1 0.0300 0.0000 ; sigma-hole site on Cl0 (mass 0)
[virtual_sites2]
site atom_i atom_j funct a
6 1 2 1 1.17
7 1 3 1 1.17
Well I used small positive charges along the C–Cl bonds nearer to Cl atoms as I told as classical sigma holes. My system contained 500 MeOH and 500 CH2Cl2. From energy minimization to NPT equilibriation I used these CH2Cl2 molecules with 2 sigma-holes. Now during my production run, I created two index groups, indexing EP1 and EP2 of CH2Cl2 and O of MeOH. Then I used the command: “energygrps =MeOH_O CH2Cl2_EP1 CH2Cl2_EP2” to get segregated interaction energy values between each two of the 3 index groups. At the end of production run, you can find segregated Coulomb SR, LJ SR etc energy in between the two specific groups like MeOH-O and CH2Cl2-EP1…like that. But in my case I find the interaction energy between EP1 and 2 and O of MeOH totally ZERO!!! Like the EP sites don’t even exist!! Am I doing the indexing wrong? Or is there some other problem? Thnx in advance.
After you suggested, I searched for all other pairs. And yes all are zero. Only the interaction energies with itself ain’t zero. So I guess the problem is in the energygrps command I’m using or in the indexing? I grouped similar types of atoms under corresponding index groups. I’ve attached an image. And many, many thanks for answering my questions. Big help!!!
