<div>Hi! I'm a postgraduate student from Malaysia and currently facing energy minimization problem for my membrane system.</div>
<div>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:-</div>
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<div>Initiating Steepest Descents<br>Max number of connections per atom is 25<br>Total number of connections is 84976<br>Max number of graph edges per atom is 4<br>Total number of graph edges is 22896<br>Going to use C-settle (2460 waters)<br>
wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897<br>rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1<br>Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009<br>Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+03<br> Number of steps = 100<br>Grid: 11 x 11 x 11 cells<br> Step Time Lambda<br> 0 0.00000 0.00000</div>
<div> Energies (kJ/mol)<br> Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih.<br> 1.64082e+05 1.71875e+04 4.06560e+03 6.45104e+03 8.36392e+03<br> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.<br>
2.12067e-314 2.12067e-314 -1.58963e+04 -1.05392e+05 -1.15292e+05<br><font style="BACKGROUND-COLOR: #ff6666"> Position Rest</font>. Potential Pressure (bar)<br> <font color="#ff9966"> 0.00000e+00</font> -3.64297e+04 nan</div>
<div><br>-------------------------------------------------------<br>Program mdrun_d, VERSION 4.0.5<br>Source code file: nsgrid.c, line: 357</div>
<div>Range checking error:<br>Explanation: During neighborsearching, we assign each particle to a grid<br>based on its coordinates. If your system contains collisions or parameter<br>errors that give particles very high velocities you might end up with some<br>
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>put these on a grid, so this is usually where we detect those errors.<br>Make sure your system is properly energy-minimized and that the potential<br>
energy seems reasonable before trying again.</div>
<div>Variable ci has value -2147483648. It should have been within [ 0 .. 1331 ]</div>
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<div>the position restraint energy is 0 as highlighted. Here's the position restraint file :-</div>
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<div>[ position_restraints ]<br>; atom type fx fy fz<br> 1 1 1000 1000 5000<br> 5 1 1000 1000 1000<br> 6 1 1000 1000 1000<br> 7 1 1000 1000 1000<br> 8 1 1000 1000 1000<br>
9 1 1000 1000 1000<br> 10 1 1000 1000 1000</div>
<div>......</div>
<div><br>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).</div>
<div>I think that the position restraint is not working fine here. Is there anyways to solve this? did I miss out something here? </div>
<div>I would be grateful if anyone can advice me on this.</div>
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