[gmx-users] Cannot Generate .gro and .cpt files after running nvt

[Chenyu Liu]

Hi Dallas,
Thanks for reaching out to me about this issue and I really appreciate it.
This is the error message from the gromacs I found:

step 4950: One or more water molecules can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates

/var/spool/torque/mom_priv/jobs/17217805.mesabim1.msi.umn.edu.SC: line 47:
14959 Segmentation fault      (core dumped) gmx_mpi mdrun -deffnm nvt


Currently, I switch to the mdp files generated from CHARMM-GUI to run
the simulation and it works smoothly.

Thanks again!

Chenyu Liu


On Tue, Sep 24, 2019 at 5:06 PM Dallas Warren <dallas.warren at monash.edu>
wrote:

> Check the log file output, plus the error output. The latter if you are
> running the command straight from the terminal will be printed to the
> screen, or if on a cluster then it will be in the the queuing system log
> file. That will tell you what is happening, and a likely reason why.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Wed, 25 Sep 2019 at 04:39, Chenyu Liu <liu00554 at umn.edu> wrote:
>
> > Dear gmx-users,
> > I was working on my first project as a student and I modified the nvt.mdp
> > file from http://www.mdtutorials.com/gmx/lysozyme/Files/nvt.mdp and
> > changed
> > the constrain algorithm from LINCS to SHAKE. However after running the
> > commands I cannot obtain the .gro file and .cpt file, which is needed for
> > the npt equilibrium steps. I was wondering what's wrong with it.
> > The force field I used is  charmm36-mar2019 from MacKerell group
> > http://mackerell.umaryland.edu/charmm_ff.shtml
> >
> > The mdp file I run is as follows:
> >
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> >
> > *title                   = CHARMM PKA NVT equilibrationdefine
> >    = -DPOSRES  ; position restrain the protein; Run parametersintegrator
> >            = md        ; leap-frog integratornsteps                  =
> > 5000000   ; 2 * 5000000 = 10 nsdt                      = 0.002     ; 2
> fs;
> > Output controlnstxout                 = 500       ; save coordinates
> every
> > 1.0 psnstvout                 = 500       ; save velocities every 1.0
> > psnstenergy               = 500       ; save energies every 1.0 psnstlog
> >                = 500       ; update log file every 1.0 ps; Bond
> > parameterscontinuation            = no        ; first dynamics
> > runconstraint_algorithm    = shake     ; Shake Algorithm is
> > Appliedconstraints             = h-bonds   ; bonds involving H are
> > constrained; Nonbonded settingscutoff-scheme           = Verlet    ;
> > Buffered neighbor searchingns_type                 = grid      ; search
> > neighboring grid cellsnstlist                 = 10        ; 20 fs,
> largely
> > irrelevant with Verletrcoulomb                = 1.0       ; short-range
> > electrostatic cutoff (in nm)rvdw                    = 1.0       ;
> > short-range van der Waals cutoff (in nm)DispCorr                =
> EnerPres
> >  ; account for cut-off vdW scheme; Electrostaticscoulombtype
>  =
> > PME       ; Particle Mesh Ewald for long-range electrostaticspme_order
> >           = 4         ; cubic interpolationfourierspacing          = 0.16
> >    ; grid spacing for FFT; Temperature coupling is ontcoupl
> >  = V-rescale             ; modified Berendsen thermostattc-grps
> >     = Protein Non-Protein   ; two coupling groups - more accuratetau_t
> >               = 0.1     0.1           ; time constant, in psref_t
> >         = 300     300           ; reference temperature, one for each
> > group, in K; Pressure coupling is offpcoupl                  = no
> ;
> > no pressure coupling in NVT; Periodic boundary conditionspbc
> >       = xyz       ; 3-D PBC; Dispersion correctionDispCorr
>   =
> > EnerPres  ; account for cut-off vdW sch; Velocity generationgen_vel
> >         = yes       ; assign velocities from Maxwell distributiongen_temp
> >              = 300       ; temperature for Maxwell distributiongen_seed
> >            = -1        ; generate a random seed*
> >
> > Instead of getting the gro and cpt files, I got some files such as
> > core.2581 and step3152c.pdb.
> >
> > I would really appreciate it if you could help me!
> > Thanks!
> > Chenyu Liu
> > --
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