<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV>Dear colleagues,<BR> <BR> I am simulating a phosphorylated protein embedded in waterbox. </DIV>
<DIV>When I try running mdrun, I get a LINCS warning.<BR> <BR>Does this mean that I have go back to the CG-EM step and use the double <BR>precision libs?<BR><BR>The md.log file reads:<BR><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><BR>Step -2, time -0.004 (ps) LINCS WARNING<BR>relative constraint deviation after
LINCS:<BR>max 0.342830 (between atoms 698 and 700) rms 0.028042<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR> 687 689 34.6 0.1776 0.1937 0.1330<BR> 689 690 34.7 0.1079 0.0919 0.1000</DIV>
<DIV> --------------------------------------------------<BR>Constraining the coordinates at t0-dt (step -1)<BR> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.095785 3223 3224 0.006243<BR> After LINCS 0.858278 3397 3398 0.016634<BR><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>Started mdrun on node 0 Tue Sep 11 07:03:49 2007<BR><BR>Initial temperature: 420.799 K</DIV>
<DIV> </DIV>
<DIV> Step Time Lambda </DIV>
<DIV> 0 0.00000 0.00000 </DIV>
<DIV> </DIV>
<DIV>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><BR>Step 0, time 0 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 227.983810 (between atoms 3223 and 3224) rms 4.787549<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><BR>Constraint error in algorithm Lincs at step 0<BR><BR>Step 1, time 0.002 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 227.983810 (between atoms 3223 and 3224) rms 4.787549<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><BR>Constraint error in algorithm Lincs at step 1</DIV>
<DIV><EM> </EM>and the simulation stops at step 1.<BR><BR> Do I have to modify my md.mdp to remedy this?<BR> <BR> Your advice is appreciated.<BR> <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>
<DIV><I>title = Full mdp run sample<BR></I><I>cpp = /lib/cpp</I></DIV>
<DIV><I>constraints = all-bonds<BR></I><I>integrator = md<BR></I><I>dt = 0.002 ; ps !</I><I><BR></I><I>steps = 2000000000 ; total 100 ns<BR></I><I>;nstcomm = 1<BR></I><I>nstxout = 500<BR></I><I>nstvout = 1000<BR></I><I>nstfout = 0<BR></I><I>nstlog
= 500<BR></I><I>nstenergy = 500<BR></I><I>nstlist = 10<BR></I><I>ns_type = grid<BR></I><I>rlist = 0.9<BR></I><I>coulombtype = PME<BR></I><I>rcoulomb = 0.9<BR></I><I>rvdw = 1.4<BR></I><I>; Berendsen temperature coupling is on in two groups<BR></I><I>Tcoupl =
berendsen<BR></I><I>tau_t = 0.1 0.1 0.1<BR></I><I>tc-grps = protein sol NA+<BR></I><I>ref_t = 300 300 300<BR></I><I>; Energy monitoring<BR></I><I>energygrps = protein sol NA+<BR></I><I>; Pressure coupling is on<BR></I><I>Pcoupl = berendsen<BR></I><I>pcoupltype =
anisotropic<BR></I><I>tau_p = 0.5 </I></DIV>
<DIV><I>compressibility = 4.5e-5 <BR></I><I>ref_p = 1.0 </I></DIV>
<DIV><I>; Generate velocites is on at 300 K.<BR></I><I>gen_vel = no</I></DIV>
<DIV><I>gen_temp = 300.0<BR></I><I>gen_seed = 173529</I><I><BR></DIV></I>
<DIV> </DIV>
<DIV> </DIV></div><br>
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