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

[Chenyu Liu]

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:









































*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