[gmx-users] Unusual Blow up

Justin Lemkul jalemkul at vt.edu
Tue Sep 1 23:23:42 CEST 2015

On 9/1/15 9:40 AM, Nima Soltani 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

You'll have to describe in exact detail what you're doing.  It's very easy to 
break a polarizable model.  What are the sources of the parameters?  Have these 
parameters been validated in the context of TIP3P?  This sounds like a very 
weird combination to me, to have part of the system polarizable and the rest not.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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