Hi! I'm a postgraduate student from Malaysia and currently facing energy minimization problem for my membrane system. I'm trying to perform energy minimization for an empty POPC membrane with position restraint on the lipid. Minimization stop due to inf Fmax. And I noticed that in the log file as below:-
Initiating Steepest Descents Max number of connections per atom is 25 Total number of connections is 84976 Max number of graph edges per atom is 4 Total number of graph edges is 22896 Going to use C-settle (2460 waters) wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897 rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1 Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009 Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 100 Grid: 11 x 11 x 11 cells Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih. 1.64082e+05 1.71875e+04 4.06560e+03 6.45104e+03 8.36392e+03 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 2.12067e-314 2.12067e-314 -1.58963e+04 -1.05392e+05 -1.15292e+05 Position Rest. Potential Pressure (bar) 0.00000e+00 -3.64297e+04 nan ------------------------------------------------------- Program mdrun_d, VERSION 4.0.5 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 1331 ] the position restraint energy is 0 as highlighted. Here's the position restraint file :- [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 5000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 10 1 1000 1000 1000 ...... whereby the restraint energy is 1000kcal/mol in x, y and z plane. In the log file the position restraint energy is stated as 0.0000e+00 (as highlighted above). I think that the position restraint is not working fine here. Is there anyways to solve this? did I miss out something here? I would be grateful if anyone can advice me on this.
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