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

[Dallas Warren]

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
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> 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*
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> Instead of getting the gro and cpt files, I got some files such as
> core.2581 and step3152c.pdb.
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> I would really appreciate it if you could help me!
> Thanks!
> Chenyu Liu
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