[gmx-users] Forces are large - How to track down the culprit

[Shay Amram]

Greetings dear Gromacs users,

 

I have recently been simulating a POPG membrane* in water (SPC). Several of
my simulations after running well into the 10ns and 20ns are sometimes
getting a "Forces for atom X are large".  

I'm rather unsure as to the cause of this situation. Moreover, as far as I
can tell from viewing the simulation, the system does NOT explode (as may be
suggested by wiki.gromacs and some previous answers to this kind of
situation). The rest of the simulation looks much as it did in the
beginning.

I would be interested (and thankful!) to hear any of your opinions as to why
I'm getting this message (or how to catch the culprit), and more
importantly, how to prevent it from happening in the future. 

The following below includes the error message as well as my md.mdp
settings.

Lipid membrane (64 L and 64 D popg molecules) are coupled together, also
solvent is coupled together with ions.  Pressure is semiisotropic.

 

Thanks a lot, 

Shay. 

 

Beginning of Warning message (the atom in reference is C4 of L-POPG
molecule).

---------------------------------------------------------

Reading frame     600 time 6000.000   Warning at frame 693. Forces for atom
3820 are large (-10016.3)

Last frame       1000 time 10000.000

---------------------------------------------------------

 

md.mdp settings

---------------------------------------------------------

title               =  Full MD

cpp                 =  /usr/bin/cpp

constraints         =  all-bonds

integrator          =  md

dt                  =  0.002    ; ps !

nsteps              =  5000000    ; 10000 ps run

nstxout             =  5000

nstvout             =  5000

nstfout             =  5000

pbc                 =  xyz

nstlist             =  10

ns_type             =  grid

rlist               =  1.2

coulombtype         =  PME

rcoulomb            =  1.2

vdw-type            =  Cut-off

rvdw                =  1.2

gen_vel             =  no

fourierspacing      =  0.1

fourier_nx          =  0

fourier_ny          =  0

fourier_nz          =  0

pme_order           =  4

; Berendsen temperature coupling is on in two groups

Tcoupl              =  berendsen

tau_t               =  0.1      0.1

tc-grps             =  sol_ions popg_membrane_DL

ref_t               =  310      310

; Pressure coupling is on

Pcoupl              =  berendsen

pcoupltype          =  semiisotropic

tau_p               =  1.0      1.0

compressibility     =  4.5e-5   0

ref_p               =  1.0      1.0

---------------------------------------------------------

 

* POPG membrane refers to the following article (Atomic-Scale Structure and
Electrostatics of Anionic Palmitoyloleoylphosphatidylglycerol Lipid Bilayers
with Na1 Counterions, Biophysical Journal Volume 92 February 2007 1114-1124
)

 

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