[gmx-users] Final structure broken

[Dhumal, Nilesh]

Hello Users,


I am running simulation for 1-hexyl-3-methylimidazolium chloride ionic liquid using GROMACS - 2018.1. Simulation box have 128 ion pairs. Initial conformation was minimized and later performed NVT and NPT simulation (1.25ns )at 400K respectively.

gmx grompp -f nvt_equ_400.mdp -c initial.pdb -p  hmi_cl_128.top -o nvt_400.tpr
gmx mdrun -s nvt_400.tpr -c nvt_400.pdb -g nvt_400.log


gmx grompp -f npt_equ_400.mdp -c  nvt_400.pdb -p  hmi_cl_128.top -o npt_400.tpr
gmx mdrun -s npt_400.tpr -c npt_400.pdb -g npt_400.log

gmx grompp -f npt_equ_350.mdp -c npt_400.pdb -p  hmi_cl_128.top -o 350.tpr
gmx mdrun -s 350.tpr -c eq.pdb -g eq.log
gmx trjconv -f traj.gro -o traj.gro -s 350.tpr  -pbc nojump



NPT simulation (1.25ns) at 350 was performed using the final structure form NPT 400 K simulation. Bonds were broken in the final structure. . trr file converted into .gro format and visualized in VMD.

gmx trjconv -f traj.gro -o traj.gro -s 350.tpr  -pbc nojump

All bonds were fine in the trajectory. There are broken only in final structure at 350K. Pasted .mdp file for reference. Could you please whats wrong.  I tested the simulation with same parameters using GROMACS-4.5.5 version. Structure was fine.


mdp file


title               =  cpeptid position restraining
cpp                 =  /usr/bin/cpp
constraints         =  none
integrator          =  md
dt                  =  0.001    ; ps !
nsteps              =  10000000      ; total 1.0 ps.
nstxout             =  10000
nstvout             =  0
nstfout             =  0
nstcomm             =  1000
nstlog              =  1000
nstcalcenergy       =  1000
nstenergy           =  1000
nstlist             =  10
ns-type             =  grid
rlist               =  1.4
coulombtype         = PME
vdwtype             = Switch;  cut-off
;vdw-modifier        =  Force-switch
rcoulomb            =  1.4
rvdw                =  1.4
rvdw-switch         =  1.0
;cutoff-scheme       =  Verlet
fourierspacing      = 0.10
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order           = 4
ewald_rtol          = 1e-6
optimize_fft        = yes
; Berendsen temperature coupling is on
Tcoupl =  Nose-Hoover
tau_t = 1.0
tc-grps  =system
ref_t = 350.0
; Pressure coupling is  on
Pcoupl              = parrinello-rahman  ;no;MTTK ;
pcoupltype          = isotropic
tau_p               =  3.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
;gen_vel             = no;  yes
;gen_temp            =  350.0
;gen_seed            =  173529