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

[Justin Lemkul]

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
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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