[gmx-users] about equilibration and minimization!

zzhwise1 zzhwise1 at 163.com
Sun Sep 17 04:18:14 CEST 2006

i have conformed my system well,then i used the l-bfgs to minimize it for 5000 steps,but it stopped at 245th steps,for system han no change,then ,i used steep but no used,it show
"<FONT size=2>Too many LINCS warnings (10997) - aborting to avoid logfile runaway.                                                                      <BR>This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations.<BR>If you know what you are doing you can adjust the lincs warning threshold                                                                 <BR>in your mdp file, but normally it is better to fix the problem.                                                                           <BR>                                                                                                                                          <BR></FONT><FONT size=4>---------------------</FONT></FONT></DIV>
<DIV><FONT size=4><FONT size=4>  i want to know what the real equilibration,do the l-bfgs and steep not?            </FONT></FONT></DIV>
<DIV><FONT size=4><FONT size=4></FONT></FONT> </DIV>
<DIV><FONT size=4><FONT size=4>also ,when  use MD it show the top and the gro's coordinate not match?why? my gro was correct under other mdp in grompp!</FONT></FONT></DIV>
<DIV><FONT size=4>could anyone help me ?</FONT></DIV>
<DIV><FONT size=4> thanks a lot!                                                                                         <BR></DIV></FONT>
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