[gmx-users] Unusual Blow up

[Nima Soltani]

Justin Lemkul <jalemkul at ...> writes:

> 
> 
> 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
> 

Thank you dear Vitaly V. Chaban and  dear Justin for your suggestions

Vitaly I am simulating these types of system for nearly a year and it was
working with 1 fs dt and it should not be the problem , Besides i need to
simulate the system for more than 320ns and it is not feasible to reduce dt
more.

Yes dear Dr. Lemkul 
force field is a combination of valid and tested parameters 

DOI:10.1021/ct301018m
DOI:10.1021/la402839q 

The strange thing about this error is that Ag(111) surface was successfully
simulated and the result was reasonable however the same procedure for
Ag(100) leads to this error !