[gmx-users] Final structure broken

[Justin Lemkul]

On 5/14/18 8:42 PM, Dhumal, Nilesh wrote:
> 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.

The final structure is normally "broken" and is fixed simply with

gmx trjconv -s md.tpr -f confout.gro -o fix.gro -pbc whole

Molecules should always be made whole before removing jumps.

-Justin

>
> 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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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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