[gmx-users] Unusual Blow up

Nima Soltani nima.slt at gmail.com
Tue Sep 1 15:40:34 CEST 2015

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:

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.

More information about the gromacs.org_gmx-users mailing list