<html><div style='background-color:'><DIV>Yiannis wrote:</DIV>
<DIV>I have problems equilibrating the box.<BR>Actually, it "looks" equilibrated. I mean that I begin a 1ns simulation and for <BR>the first 221690 steps (1fs each, so the first 221.69ps) the density, <BR>temperature, energies (KE, PE, LJ, Coulomb, dispersion, LR etc), volume, x,y,z, <BR>of the box seam stable oscillating around reasonable values. Looking at the <BR>ngmx animation, everything looks fine as well. But then, after step 221690 I <BR>get a crash. Here is the output:<BR><BR>********************begin mdrun output**************<BR>Warning: Only triclinic boxes with the first vector parallel to the x-axis and <BR>the <BR>second vector in the xy-plane are supported.<BR> Box (3x3):<BR> Box[ 0]={ NaN, NaN, !<BR> NaN<BR>}<BR> Box[ 1]={ NaN, NaN, NaN}<BR> Box[ 2]={ NaN, NaN, NaN}<BR> Can not fix pbc.<BR>Warning: Only triclinic boxes with the first vector parallel to the x-axis and <BR>the <BR>second vector in the xy-plane are supported.<BR> Box (3x3):<BR> Box[ 0]={ NaN, NaN, NaN}<BR> Box[ 1]={ NaN, NaN, NaN}<BR> Box[ 2]={ NaN, NaN, NaN}<BR> Can not fix pbc.<BR>Warning: Only triclinic boxes with the first vector parallel to the x-axis and <BR>the <BR>second vector in the xy-plane are supported.<BR> Box (3x3):<BR> Box[ 0]={ NaN, NaN, NaN}<BR> Box[ 1]={ NaN, NaN, NaN}<BR> Box[ 2]={ NaN, NaN, NaN}<BR> !<BR> Can not f<BR>ix pbc.<BR>Warning: Only triclinic boxes with the first vector parallel to the x-axis and <BR>the <BR>second vector in the xy-plane are supported.<BR> Box (3x3):<BR> Box[ 0]={ NaN, NaN, NaN}<BR> Box[ 1]={ NaN, NaN, NaN}<BR> Box[ 2]={ NaN, NaN, NaN}<BR> Can not fix pbc.<BR>Warning: Only triclinic boxes with the first vector parallel to the x-axis and <BR>the <BR>second vector in the xy-plane are supported.<BR> Box (3x3):<BR> Box[ 0]={ NaN, NaN, NaN}<BR> Box[ 1]={ NaN, NaN, NaN}<BR> Box[ 2]={ NaN, NaN, NaN}<BR> Can not fix pbc.<BR>Warning: Only triclinic boxes with the first vector parallel to the x-axis and <BR>the <BR>second vector in the xy-plane are supported.<BR> !<BR>Box (3x3):<BR><BR> Box[ 0]={ NaN, NaN, NaN}<BR> Box[ 1]={ NaN, NaN, NaN}<BR> Box[ 2]={ NaN, NaN, NaN}<BR> Can not fix pbc.<BR>Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]<BR>********************end mdrun output**************<BR>Of course I looked at the box size but at the last recorded step it is OK. Any<BR>ideas, suggestions, help?</DIV>
<DIV> </DIV>
<DIV>Yiannis</DIV>
<DIV><BR> I think it might be help just turning off pbc, i.e. pbc=off. But I don't know whether it makes sense.</DIV>
<DIV>Cheers,</DIV>
<DIV>Songbai Liu</DIV>
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