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

[Chenyu Liu]

Hi Justin,
Thanks for your helpful reply and I really appreciate it! Actually, I was
about to post the Error message from the output. It does crash.
The message is as follows:

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

I will be looking into the online manual for charmm force field for
solution. And, again, thanks for your generous help!
Chenyu Liu

On Tue, Sep 24, 2019 at 1:49 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/24/19 2:44 PM, Chenyu Liu wrote:
> > Sorry about the format issue in the previous email. I hope this will give
> > you a better view for the mdp file I use to run nvt simulations.
> > title                   = CHARMM PKA NVT equilibration
> >
> > define                  = -DPOSRES  ; position restrain the protein
> >
> > ; Run parameters
> >
> > integrator              = md        ; leap-frog integrator
> >
> > nsteps                  = 5000000   ; 2 * 5000000 = 10 ns
> >
> > dt                      = 0.002     ; 2 fs
> >
> > ; Output control
> >
> > nstxout                 = 500       ; save coordinates every 1.0 ps
> >
> > nstvout                 = 500       ; save velocities every 1.0 ps
> >
> > nstenergy               = 500       ; save energies every 1.0 ps
> >
> > nstlog                  = 500       ; update log file every 1.0 ps
> >
> > ; Bond parameters
> >
> > continuation            = no        ; first dynamics run
> >
> > constraint_algorithm    = shake     ; Shake Algorithm is Applied
> >
> > constraints             = h-bonds   ; bonds involving H are constrained
> >
> > ; Nonbonded settings
> >
> > cutoff-scheme           = Verlet    ; Buffered neighbor searching
> >
> > ns_type                 = grid      ; search neighboring grid cells
> >
> > nstlist                 = 10        ; 20 fs, largely irrelevant with
> Verlet
> >
> > rcoulomb                = 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
>
> You're taking this input file from my tutorial - don't. The settings
> here are for OPLS, not CHARMM. The proper settings for CHARMM are
> available in the GROMACS online manual.
>
>  From your previous message you said:
>
> "Instead of getting the gro and cpt files, I got some files such as
> core.2581 and step3152c.pdb."
>
> Your simulation crashed. Check for relevant error messages in the .log
> file and stdout/stderr and consult:
>
> http://manual.gromacs.org/current/user-guide/terminology.html#blowing-up
>
>
> http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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