<div class="gmail_quote"><div>Hi gromacs users,</div><div>I am tying to minimize a protein through grolacs 4.5.5 double precision. </div><div>If I try to minimize it without virtual site, everythin goes fine but if I add virtual site through:</div>
<div><br></div><div>pdb2gmx -vsite hydrogens -chainsep id -f Aqui_model.pdb -ff charmm27 -water tip3p -posrefc 1000 -v -rtpres</div><div>I obtain the following output:</div><div><br></div><div><b>Steepest Descents:</b></div>
<div><b> Tolerance (Fmax) = 1.00000e+03</b></div><div><b> Number of steps = 1000</b></div><div><b>Step= 0, Dmax= 1.0e-02 nm, Epot= 1.21621e+06 Fmax= 2.24275e+08, atom= 12592</b></div><div><b>Step= 1, Dmax= 1.0e-02 nm, Epot= -4.92685e+05 Fmax= 1.05309e+07, atom= 12585</b></div>
<div><b>Step= 2, Dmax= 1.2e-02 nm, Epot= -6.65927e+05 Fmax= 2.33570e+06, atom= 12586</b></div><div><b>Step= 3, Dmax= 1.4e-02 nm, Epot= -7.19859e+05 Fmax= 2.16295e+06, atom= 12585</b></div><div><b>Step= 4, Dmax= 1.7e-02 nm, Epot= -7.53908e+05 Fmax= 8.32452e+05, atom= 12586</b></div>
<div><b>Step= 5, Dmax= 2.1e-02 nm, Epot= -7.75691e+05 Fmax= 9.90803e+05, atom= 12585</b></div><div><b>Step= 6, Dmax= 2.5e-02 nm, Epot= -7.98119e+05 Fmax= 9.99586e+04, atom= 12730</b></div><div><b>Step= 7, Dmax= 3.0e-02 nm, Epot= -8.47120e+05 Fmax= 7.37766e+05, atom= 12585</b></div>
<div><b><br></b></div><div><b>Step 8, time 0.008 (ps) LINCS WARNING</b></div><div><b>relative constraint deviation after LINCS:</b></div><div><b>rms 0.000009, max 0.000105 (between atoms 12731 and 12728)</b></div><div><b>bonds that rotated more than 30 degrees:</b></div>
<div><b> atom 1 atom 2 angle previous, current, constraint length</b></div><div><b> 12586 12585 32.1 0.0936 0.0936 0.0936</b></div><div><b>Step= 8, Dmax= 3.6e-02 nm, Epot= -8.55218e+05 Fmax= 5.79704e+04, atom= 12585</b></div>
<div><b>Step= 9, Dmax= 4.3e-02 nm, Epot= -8.92739e+05 Fmax= 1.11595e+05, atom= 12585</b></div><div><b><br></b></div><div><b>Step 10, time 0.01 (ps) LINCS WARNING</b></div><div><b>relative constraint deviation after LINCS:</b></div>
<div><b>rms 0.000045, max 0.000529 (between atoms 12731 and 12728)</b></div><div><b>bonds that rotated more than 30 degrees:</b></div><div><b> atom 1 atom 2 angle previous, current, constraint length</b></div><div><b> 12586 12585 46.3 0.0934 0.0936 0.0936</b></div>
<div><b> 12731 12730 31.3 0.0936 0.0936 0.0936</b></div><div><b>Step= 10, Dmax= 5.2e-02 nm, Epot= -9.06732e+05 Fmax= 8.54476e+04, atom= 12730</b></div><div><b><br></b></div><div><b>Step 11, time 0.011 (ps) LINCS WARNING</b></div>
<div><b>relative constraint deviation after LINCS:</b></div><div><b>rms 0.000184, max 0.002545 (between atoms 12731 and 12728)</b></div><div><b>bonds that rotated more than 30 degrees:</b></div><div><b> atom 1 atom 2 angle previous, current, constraint length</b></div>
<div><b> 12731 12730 63.6 0.0936 0.0937 0.0936</b></div><div><b>Step= 11, Dmax= 6.2e-02 nm, Epot= -9.23686e+05 Fmax= 1.13169e+05, atom= 15031</b></div><div><b>Step= 12, Dmax= 7.4e-02 nm, Epot= -9.23888e+05 Fmax= 3.23226e+05, atom= 15031</b></div>
<div><b><br></b></div><div><b>Step 13, time 0.013 (ps) LINCS WARNING</b></div><div><b>relative constraint deviation after LINCS:</b></div><div><b>rms 0.054250, max <a href="tel:0.852392" value="+390852392" target="_blank">0.852392</a> (between atoms 12731 and 12728)</b></div>
<div><b>bonds that rotated more than 30 degrees:</b></div>
<div><b> atom 1 atom 2 angle previous, current, constraint length</b></div><div><b> 12736 12728 142.1 0.1908 0.1192 0.1681</b></div><div><b> 12737 12728 146.1 0.1966 0.1354 0.1681</b></div><div>
<b><br></b></div><div><b>Back Off! I just backed up step13b_n4.pdb to ./#step13b_n4.pdb.1#</b></div><div><b><br></b></div><div><b>Back Off! I just backed up step13c_n4.pdb to ./#step13c_n4.pdb.1#</b></div><div><b>Wrote pdb files with previous and current coordinates</b></div>
<div><b>Step= 13, Dmax= 8.9e-02 nm, Epot= -9.22947e+05 Fmax= 2.12030e+06, atom= 12728</b></div><div><b>Step 14, time 0.014 (ps) LINCS WARNING</b></div><div><b>relative constraint deviation after LINCS:</b></div><div><b>rms 0.060515, max 0.946017 (between atoms 12731 and 12728)</b></div>
<div><b>bonds that rotated more than 30 degrees:</b></div><div><b> atom 1 atom 2 angle previous, current, constraint length</b></div><div><b> 12736 12728 141.9 0.1908 0.1315 0.1681</b></div><div><b> 12737 12728 149.5 0.1966 0.1435 0.1681</b></div>
<div><b><br></b></div><div><b>Back Off! I just backed up step14b_n4.pdb to ./#step14b_n4.pdb.1#</b></div><div><b><br></b></div><div><b>Back Off! I just backed up step14c_n4.pdb to ./#step14c_n4.pdb.1#</b></div><div><b>Wrote pdb files with previous and current coordinates</b></div>
<div><b>Step= 14, Dmax= 4.5e-02 nm, Epot= -9.25189e+05 Fmax= 2.68447e+06, atom= 12728</b></div><div><b><br></b></div><div><b>Step 15, time 0.015 (ps) LINCS WARNING</b></div><div><b>relative constraint deviation after LINCS:</b></div>
<div><b>rms 1.882205, max 21.643097 (between atoms 12736 and 12728)</b></div><div><b>bonds that rotated more than 30 degrees:</b></div><div><b> atom 1 atom 2 angle previous, current, constraint length</b></div><div><b> 12730 12728 173.7 0.3265 3.7204 0.1681</b></div>
<div><b> 12731 12728 167.1 0.3272 3.6402 0.1681</b></div><div><b> 12736 12728 159.7 0.1315 3.8068 0.1681</b></div><div><b> 12737 12728 157.0 0.1435 3.7391 0.1681</b></div><div><b> 12731 12730 48.9 0.0913 0.1124 0.0936</b></div>
<div><b> 12737 12736 38.5 0.0960 0.1056 0.0936</b></div><div><b><br></b></div><div><b>Back Off! I just backed up step15b_n4.pdb to ./#step15b_n4.pdb.1#</b></div><div><b><br></b></div><div><b>Back Off! I just backed up step15c_n4.pdb to ./#step15c_n4.pdb.1#</b></div>
<div><b>Wrote pdb files with previous and current coordinates</b></div><div><b>Warning: 1-4 interaction between 12732 and 12741 at distance 1.975 which is larger than the 1-4 table size 1.800 nm</b></div><div><b>These are ignored for the rest of the simulation</b></div>
<div><b>This usually means your system is exploding,</b></div><div><b>if not, you should increase table-extension in your mdp file</b></div><div><b>or with user tables increase the table size</b></div><div><b><br></b></div>
<div><b>A list of missing interactions:</b></div><div><b> Connect Bonds of 7310 missing 1</b></div><div><b> U-B of 21832 missing 3</b></div><div><b> Proper Dih. of 35369 missing 12</b></div>
<div><b> LJ-14 of 36933 missing 10</b></div><div><b> exclusions of 151813 missing 20</b></div><div><b><br></b></div><div><b>-------------------------------------------------------</b></div>
<div><b>Program mdrun_d, VERSION 4.5.4</b></div><div><b>Source code file: domdec_top.c, line: 173</b></div><div><b><br></b></div><div><b>Software inconsistency error:</b></div><div><b>Some interactions seem to be assigned multiple times</b></div>
<div><b>For more information and tips for troubleshooting, please check the GROMACS</b></div><div><b>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></b></div>
<div><b>-------------------------------------------------------</b></div><div><b><br></b></div><div><b>"Ich Bin Ein Berliner" (J.F. Kennedy)</b></div><div><br></div><div><br></div><div>I tryed both with constrain then without, but I obtain always the same result.</div>
<div><br></div><div>The files I have used to run the minimization can be downloaded from <a href="http://160.80.35.105/download/vsite.tgz">http://160.80.35.105/download/vsite.tgz</a> </div><div>Has anyone of you any idea?</div>
<div> </div><div> Francesco</div>
<span class="HOEnZb"><font color="#888888"><div> </div>
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