[gmx-users] System blowing up in final MD run

[Tsjerk Wassenaar]

Hi Deep,

What force field? What system? How many cores? Did you try running on one?
What error? Did pdb2gmx or grompp give any warnings?

Cheers,

Tsjerk

On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <hypergenetics at gmail.com>
wrote:

> Hello,
> My system is blowing up for the protein carbohydrate solvent complex. I
> have attached the mdp file below. The NPT and NVT were in good accordance
> to tutorial listed by Justin. 'Please help me solve the issue.
> title       = CD44  complex MD simulation
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 10000000    ; 0.001 * 1000000 = 10000 ps (10 ns)
> dt          = 0.001     ; 1 fs
> ; Output control
> nstxout             = 50000         ; suppress .trr output
> nstvout             = 50000         ; suppress .trr output
> nstenergy           = 50000    ; save energies every 1000.0 ps
> nstlog              = 50000      ; update log file every 1000.0 ps
> nstxtcout = 50000
> xtc_precision = 1000
> energygrps          = Protein LIG SOL
> ; Bond parameters
> continuation    = yes           ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid      ; search neighboring grid cells
> nstlist         = 1        ;
> rcoulomb        = 0.81
> rvdw            = 0.81
> coulombtype     = Cut-off       ; Particle Mesh Ewald for long-
> vdwtype        = cut-off
> rlistlong      = 1.4
> epsilon-rf     = 61
> rlist          = 0.8
> ; Temperature coupling is on
> tcoupl = nose-hoover            ; modified Berendsen thermostat
> tc-grps       =Protein_LIG Water_and_ions   ; two coupling groups - more
> accurate
> tau_t = 2.0  2.0        ; time constant, in ps
> ref_t = 300  300        ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl        = Parrinello-Rahman            ; Pressure coupling on in NPT
> pcoupltype        = isotropic            ; uniform scaling of box vectors
> tau_p        = 6.0            ; time constant, in ps
> ref_p        = 1.0            ; reference pressure, in bar
> compressibility     = 4.5e-5            ; isothermal compressibility of
> water, bar^-1
> refcoord_scaling    = com
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = no        ; assign velocities from Maxwell distribution
>
>
> Steepest Descents converged to Fmax < 1000 in 573 steps
> Potential Energy  = -7.58370311664555e+05
> Maximum force     =  9.53896348096555e+02 on atom 1163
> Norm of force     =  2.44608995242254e+01
>
>
> *Deep S Bhattacharya*
>
> *Graduate Research Assistant*
>
> Mohs Biomedical Imaging & Nanotechnology Group
>
> Pharmaceutical Sciences
>
> *University of Nebraska Medical Center*
>
> 4018 Eppley Science Hall  |  Omaha, NE 68198-6805
>
> office 402.559.4349  | cell 402.906.1640
>
> deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
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-- 
Tsjerk A. Wassenaar, Ph.D.