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.
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