Skip to content
This repository has been archived by the owner on Feb 15, 2022. It is now read-only.

Issues with Glycerol data generated by ligpargen #90

Open
paolobotto opened this issue Jan 10, 2022 · 0 comments
Open

Issues with Glycerol data generated by ligpargen #90

paolobotto opened this issue Jan 10, 2022 · 0 comments

Comments

@paolobotto
Copy link

Hi, I want to build a slab made of Glycerol molecules to be used as substrate for Langmuir-Blodgett simulations.
Glycerol data were obtained from LigParGen site.
Multiple molecules data were obtained with Packmol.
Software is Lammps 20 dec 2020. simulation makes use of nve ensemble.
I tried first with some 6000 molecules and I got a problem, which persisted while I was decreasing the number of molecules.
To make a long story short, I tried with 3 glycerol molecules in a 10 x 10 x 10 A° box.
Again I got an Error: "Angle atoms 2 3 6 missing on proc 0 at step 672", after abot 200 fs.
Following the trajectory with OVITO, atoms are blown away very soon. Temperature raises quickly above 100,000 °K.
This surprising behavior semms to be limited to gLycerol. Propanol and 1,3-propanediol behave normally.

I am wondering if the OPLS-AA force field for glycerol as applied by LigParGen automatic generator might be for some reason not adequate.

Any comment woul be very welcome

Paolo

Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant