[gmx-users] Final structure broken

[Quyen V. Vu]

It likely in nvt you used constraint so your structure is not so much
different from initial,
In NPT you removed constraint.
When you visualize or analyze result, you need remove boundary condition as
Justin said above

On Tue, May 15, 2018, 07:43 Dhumal, Nilesh <ndhumal at fgcu.edu> 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.
>
>
> 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
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>