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<DIV>Dear colleagues,<BR>I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning.<BR>Does this mean that I have go back to the CG-EM step and use the double <BR>precision libs?<BR>The md.log file reads:<BR><BR>Initializing LINear Constraint Solver<BR> number of constraints is 2365<BR> average number of constraints coupled to one constraint is 2.5<BR><BR> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.336565 691 696 0.033770<BR> After LINCS 0.342830 698 700 0.028042<BR><BR>Step -1,
time -0.002 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.858278 (between atoms 3397 and 3398) rms 0.016634<BR>bonds that rotated more than 30 degrees:<BR>atom 1 atom 2 angle previous, current, constraint length<BR> 3395 3398 76.2 0.1341 0.0446 0.1470<BR> 3398 3399 78.8 0.1341 0.0492 0.1470<BR>Constraint error in algorithm Lincs at step -1<BR>Grid: 10 x 10 x 10 cells<BR>Configuring nonbonded kernels....<BR>Testing x86_64 SSE supports...presents<BR> <BR> Rel. Constraint Deviation: Max between atoms RMS<BR> Before
LINCS 70.089874 1537 1456 0.559021<BR> After LINCS 29.983810 3223 3224 0.787549<BR><BR>Like this, errors showed "Constraint error in algorithm Lincs at step 0, step1" and the simulation stops at step 1. Do I have to modify my md.mdp to remedy this?<BR>Your advice is appreciated.<BR> Best regards,<BR></DIV>
<DIV>Amrita Ghosh</DIV>
<DIV>National Institute of Mental Health and Neurosciences,</DIV>
<DIV>Bangalore-29.</DIV>
<DIV>India.</DIV></DIV></DIV></DIV></div><br>
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