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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
The text was updated successfully, but these errors were encountered:
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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
The text was updated successfully, but these errors were encountered: