[gmx-users] Unusual Blow up

[Vitaly V. Chaban]

Reduce the time-step.




On Tue, Sep 1, 2015 at 10:40 AM, Nima Soltani <nima.slt at gmail.com> wrote:
> Hi everyone
> I am simulating the interactions between a small peptide and different
> metallic surfaces solvated in TIP3P water.
> So far i have simulated  3 different surfaces correctly , however the last
> surface becames unstable after nearly 2 ns of simulation.
> I did an EM step again and reduced time step to half (i.e. 0.5 fs) however
> it didn't work ... I've even set lincs-warnangle to its maximum value(=
> 90), howeer it failed again . I don't have any idea how to fix it
>
> The surface is Polarizable by using *Drude* oscillators and i think these
> oscillatoras are the cause of problems .
>
>
>    Step           Time         Lambda
>         2270000     2270.00000        0.00000
>
>    Energies (kJ/mol)
>             U-B    Proper Dih.  Improper Dih.      CMAP Dih.          LJ-14
>     3.87510e+02    6.15054e+01    1.98057e+01   -5.57740e+01    6.96654e+01
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     2.93372e+03    8.97847e+04   -6.19085e+03   -7.47168e+05    2.44969e+03
>    COM Pull En.      Potential    Kinetic En.   Total Energy    Temperature
>     1.39457e-03   -6.57708e+05    1.23026e+05   -5.34682e+05    3.09198e+02
>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    -2.03445e+02   -9.16454e+01    1.80260e-06
>
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.5
> Source code file:
> /share/apps/gromacs-5.0.5/gromacs-5.0.5/src/gromacs/mdlib/constr.c, line:
> 224
>
> Fatal error:
> Too many LINCS warnings (1000)
> If you know what you are doing you can adjust the lincs warning threshold
> in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>  Thanks in advance for any suggestions / assistance
>
> Best Regards,
> Nima Soltani
> ----------------------------------------------------------
> Graduate Student of Physical Chemistry
> Department of Chemistry,
> Sharif University of Technology.
> =================================
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