Hello everyone my Name is David and as part of my master thesis I want to calculate self-diffusion coefficients for n-alkanes (in the range of roughly 10-25 C) and aromatic hydrocarbons. (like 2-Ethylnaphthalene, Phenanthracen etc.).
For this I am working on implementing the TraPPE Explicit Hydrogen (EH) force field in Gromacs (http://chem-siepmann.oit.umn.edu/siepmann/trappe/index.html)
I tried to build a methane molecule for the first test run. The TraPPE Force Field (EH) uses virtual sites, located in the middle between the C and H atoms as Lennard-Jones-Interaction sites. I tried to implement this using the [virtual_sites2] section, however I get this error message when trying to solvate the methane. “number of coordinates in coordinate file (methane_solv.gro, 4309) does not match topology (topol.top, 4313)”
As the difference in number of coordinates is 4, I suspect the missing coordinates from my topol.top file are the 4 virtual sites. I guess I made some mistake creating the virtual sites however I can’t see what exactly.
Please find the files attached.
Please note that my major is Food Technology and I am new to the field of molecular dynamics. Every help is appreciated
Best regards
David, Master Student Chair of process systems engineering Gregor-Mendel-Straße 4 85354 Freising Germany
Thanks for the quick response!
So i have to put the V-Sites in the .gro aswell? i thought they get generated according to what i write under [virtual_site2], in my case in the middle between the Hs and Cs.
I will give it a try thanks :]
- Badges
- Science topic