Hi dear LAMMPS users and developers
I am doing a coarse-grained simulation about a toluene molecule using lammps ( LAMMPS 24 Dec 2020). I used the information in this paper and supporting information. (https://doi.org/10.1021/acs.jpcb.6b05925) Based on this paper. Here is the some information from paper:
They employed a rigid model for toluene comprising three SC4 beads (uncharged) held in a rigid isosceles triangle with interbead distances of 0.28,0.28, and 0.23 nm. Lennard-Jones interactions were switched smoothly to zero in the range 0.9-1.4 nm and . Following the standard Martini treatment of electrostatics, Coulomb interactions were shifted to zero in the range 0.0-1.4 nm and they employed a relative dielectric constant of 2.5 corresponding to a low-dielectric apolar toluene. The rigid bonds in the toluene
solvent were fixed to their equilibrium values using the LINCS algorithm. Simulations were conducted in the NPT ensemble using a Nose-́ Hoover thermostat65 and an isotropic Parrinello-
Rahman barostat to maintain pressure at P = 1 bar. The compressibility of the system was set to 9.0 × 10-5 bar-1 in toluene. Newton’s equations of motion were integrated using the leapfrog
algorithm with time step of 20 fs .
I convert the coefficients in the paper to KJ/mol and deleted the coulomb interactions, ( SC4 is uncharged) but the density is about 1.2 gr/cm^3 which is far farm 0.88 gr/cm^3.
Did I miss something in the simulation procedure? Thank you very much in advanced for your kind help.
ps : I attached the moltemplate and lammps script.
system.in.settings (296 Bytes)
system.lt (344 Bytes)
toluene.lt (1.51 KB)
toluene.txt (2.9 KB)