I am currently simulating a glucose molecule inside zeolite pore using LAMMPS (7 Aug 2019).
I am having a issue with the interaction of alcoholic hydrogen atom with the other nearby atoms. I am using OPLS forcefields for hydrogen(HO) and the value of sigma and epsilon is zero in OPLS. However, when I am using the value (sig & eps, 0.0), I see that the hydrogen is not facing any repulsive interaction (as V(L-J)=0 for any cross interaction with the hydrogen) with the nearby oxygen atom and during NVT it overlaps and blew out. Here I am using arithmetic mixing rule to incorporate cross interaction. I realized that when epsilon is zero the V(L-J) term is zero for any cross interaction with the hydrogen and so it has only Coulombic attraction. I am sure it is a common issue and as I am new to Lammps I don’t know how to solve it. It would be very helpful if anybody can suggest me a way to do this. Thank you.
please note that even with arithmetic mixing, you will always have an epsilon of 0.0 if one of the two atom types has a zero epsilon. the interaction energy is computed by geometric mixing for both, pair_modify geometric and pair_modify arithmetic. the difference is only for computing sigma.
Thank you very much Axel for you comment. I have used both arithmetic and geometric combining rules but hydrogens are overlapping with nearby oxygen atoms. This might be due to 0.0 epsilon value for cross interaction with the hydrogen atom. I checked for all the “pair modify” option, epsilon_ij is calculated to be zero if one of the epsilon value is zero. So I am little wonder how the hydrogen atom with zero epsilon value would find the repulsive interaction with other nearby atoms. Shall I have to add any extra enforcement tag to do it? I am attaching my inputs if you kindly check this once. Thank you for the help.
zeolite.txt (33 KB)
watermolecule.txt (328 Bytes)
glucose.txt (3.64 KB)
zeolite-2-mod.in (12.1 KB)
This is not a “LAMMPS problem” but a “science problem”. i have no time to solve that for you. that is your job. it sounds like the force field parameters you are using are inconsistent and/or not suitable for the system you are simulating as the symptoms you describe frequently happen, when people mix and match different parameter sets.
Thank you, Axel, for your explanation. I thought Lammps has some tag (which I am unaware) to fix the problem and enforce the bond to stay at an equilibrium distance even if the L=J parameter is zero. Anyway, thank you very much for your kind response.