[gmx-users] Final structure broken
Dhumal, Nilesh
ndhumal at fgcu.edu
Tue May 15 02:43:05 CEST 2018
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
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