[gmx-users] Unusual Blow up

Justin Lemkul jalemkul at vt.edu
Wed Sep 2 03:22:16 CEST 2015

On 9/1/15 9:19 PM, Nima Soltani wrote:
> 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 !

Most likely a problem in your topology, but absent any more useful information, 
there's nothing anyone on this list can do but guess.



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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