[gmx-users] Check for bad contacts and/or reduce the timestep

[Mark Abraham]

Hi,

Parrinello Rahman is not a great choice for the first stages of
equilbration, as suggested at e.g.
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation.
Your choice of temperature coupling groups is also an anti-pattern, e.g.
http://www.gromacs.org/Documentation/Terminology/Thermostats. These effects
are stronger when the temperature (ie KE) is increased despite a constant
time step.

Mark

On Sun, Jul 9, 2017 at 4:21 PM Md. Imrul Reza Shishir <
imrul.reza.shishir at gmail.com> wrote:

> Dear all
> I have simulated my system 7 different temperature from 300K~500K.Every
> time I simulated for 10ns. But when I run the simulation above 500K (I.e
> 530K/550K/560K) the simulation was crash in NPT equilibrium stage with
> following warning.
>
> *step XXX: Water molecule starting at atom XXXX can not be settled. Check
> for bad contacts and/or reduce the timestep if appropriate.*
>
> ​What should be cause for that?
>
> my energy minimization  ​stage:
> *minim.mdp*
> title            = OPLS Cellulose EM_steep simulation
> integrator        = steep
> emtol            = 1000.0     kJ/mol/nm
> emstep              = 0.0001
> nsteps            = 50000
> nstlist            = 10
> cutoff-scheme            = verlet
> ns-type                = grid
> coulombtype            = PME
> pme-order            = 4
> fourierspacing        = 0.12
> rlist                  = 1.2
> rlistlong            = 1.4
> rcoulomb            = 1.2
> rvdw                = 1.2
> pbc                = xyz
> periodic-molecules      = yes
> constraints            = none
> vdwtype               = Cut-off
>
> my npt equilibrium:
> *npt.mdp*
>
> title            = Cellulose OPLS-AA NPT equilibration
> define            = -DPOSRE
> integrator        = md
> nsteps            = 250000
> dt            = 0.002
> comm-mode        = Linear
> comm-grps               = System
> nstcomm            = 100
> pbc            = xyz
> nstxout            = 500
> nstvout            = 500
> nstenergy        = 500
> nstlog            = 500
> nstxout-compressed      = 500
> compressed-x-grps       = System
> cutoff-scheme       = verlet
> ns-type                = grid
> nstlist                = 10
> rlist                  = 1.2
> rlistlong            = 1.4
> coulombtype            = PME
> pme-order            = 4
> rcoulomb            = 1.2
> vdwtype               = Cut-off
> rvdw                = 1.2
> fourierspacing        = 0.12
> DispCorr        = EnerPres
> continuation        = yes
> constraint-algorithm    = lincs
> constraints            = all-bonds    ;
> lincs-iter            = 1
> lincs-order            = 4
> tcoupl            = v-rescale
> tc-grps            = Other    Water    Ion
> tau_t            = 0.1    0.1    0.1
> ref_t            = 550     550    550
> pcoupl                = Parrinello-Rahman
> pcoupltype            = isotropic
> tau-p                = 1.0
> ref-p                = 1.0
> compressibility         = 4.5e-5
> refcoord_scaling        = com        ;
>
> ; Velocity generation
> gen-vel            = no
>
>
> ​Thank you in advance. ​
>
> --
> *Md Imrul Reza Shishir*
> Master Student
> ​
> --
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