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!!!
yeah, the thing is I used MeOH and CH2Cl2 and added small massless positive charges(+0.03) along the C-Cl bonds, very close to Cl to resemble the sigma holes responsible for the halogen bonds. Now I use virtual sites to denote these sigma-holes as Extra Points in .itp file of CH2Cl2. My intention was to see the amount of energy b/w the oxygen and the EPs. Then I indexed both O and EP and used energygrps in production run, but that came as zero. So, as per your valuable suggestion, I tried the same for Cl and O just in case, but those are zero as well, and you can see it in the photo.
Can you please tell me one thing? If I wanna see the interaction energy values like Coulomb-SR, LJ-SR etc, between two specific atoms in the molecules I’m using, provided the two atoms are from different molecules, is it possible in GROMACS? Again thnx in advance!!
Yes, GROMACS can do that, although you will miss the PME mesh contribution.
But I see now that you seem to be using a 9 year old version. Maybe the issue there is that you are running on a GPU which will not give you the group contributions, but I am not sure that version had that issue. If you are running with a GPU, try running on the CPU instead.
But we recommend using the latest version of GROMACS.
Thanks, and I actually saw in the manual of 5.1.4 and they accept virtual sites! But I’ll take your suggestion and try again on a latest version. Also will I get the segragated interaction energies by the way I’m proceeding? Or should I have to do something more?
