[gmx-users] crash with LINCS WARNING

[Justin A. Lemkul]

Quoting LeeHwan-kyu <hklee910 at hotmail.com>:

>
> Dear GMX-uers,
>
> I'm simulating alpha-hemolysin channel in DMPC bilayer and water (using
> MARTINI protein FF), and my system keeps crashing with error below (even with
> very low timestep).  Energy minimization had enough negative value, and the
> initial configuration looks fine.  Could you tell me how to fix this problem?
>  Pressure and temperature coupling part in the .mdp file is also shown in
> below.   Thank you for your time and help.
> ----------------------------------------------
> There are 31270 atoms in your xtc output selection
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.020383  10588  10589   0.006135
>         After LINCS         0.000020  12597  12598   0.000006
>
>    Energies (kJ/mol)
>            Bond       G96Angle    Proper Dih.  Improper Dih.        LJ (SR)
>     1.36433e+04    7.49735e+03    9.81902e+02    2.79080e+02   -8.04502e+05
>    Coulomb (SR)      Potential    Kinetic En.   Total Energy    Temperature
>    -3.54612e+03   -7.85646e+05    3.20196e+03   -7.82444e+05    8.32579e+00
>  Pressure (bar)
>    -2.81263e+02
>
> Grid: 20 x 20 x 36 cells
> Grid: 20 x 20 x 37 cells
>
> Step 1596, time 31.92 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.059705 (between atoms 11419 and 11420) rms 0.002499
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   11419  11420   47.3    0.2700   0.2861      0.2700
>   11420  11421   51.8    0.2700   0.2630      0.2700
> -------------------------------------------
> ------------------------------------------
> tcoupl                   = berendsen
> ; Groups to couple separately =
> tc-grps                  = Protein DPP  W     ION
> ; Time constant (ps) and reference temperature (K) =
> tau_t                    = 1.0     1.0  1.0   1.0
> ref_t                    = 298     298  298   298

Coupling water and ions separately is a bad idea.  You would have seen this if
you had searched the archives; this is a very common problem.  It may not be
the root cause, but it certainly doesn't help.

Check the atoms involved in the early LINCS warnings; they will likely suggest
where your problem lies.  Sometimes even a negative potential energy doesn't
mean some elements of your system are badly placed.

-Justin

> ; Pressure coupling      =
> Pcoupl                   = berendsen
> Pcoupltype               = semiisotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p                    = 5.0  5.0
> compressibility   = 4.5e-5  4.5e-5
> ref_p                    = 1.0  1.0
> -----------------------------------------
>
> best,
> Hwankyu.
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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