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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