<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br><br>--- On <b>Thu, 16/7/09, Justin A. Lemkul <i>&lt;jalemkul@vt.edu&gt;</i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul &lt;jalemkul@vt.edu&gt;<br>Subject: Re: [gmx-users] Lincs Warning<br>To: "Discussion list for GROMACS users" &lt;gmx-users@gromacs.org&gt;<br>Date: Thursday, 16 July, 2009, 7:30 AM<br><br><div class="plainMail"><br><br>Samik Bhattacharya wrote:<br>&gt; <br>&gt; <br>&gt; --- On *Wed, 15/7/09, Mark Abraham /&lt;<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="/mc/compose?to=Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;/* wrote:<br>&gt; <br>&gt; <br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;From: Mark Abraham &lt;<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="/mc/compose?to=Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;<br>&gt;&nbsp;
 &nbsp;&nbsp;&nbsp;Subject: Re: [gmx-users] Lincs Warning<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;To: "Discussion list for GROMACS users" &lt;<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Date: Wednesday, 15 July, 2009, 5:23 PM<br>&gt; <br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Samik Bhattacharya wrote:<br>&gt;&nbsp; &nbsp; &nbsp; &gt; Hi all, i ma simulating a membrane protein, in which i am facing<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;a problem in the equilibration step. in the NVT equilibration when i<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;am running the mdrun command i am getting a msg like<br>&gt;&nbsp; &nbsp; &nbsp; &gt;<br>&gt;&nbsp; &nbsp; &nbsp; &gt; Program mdrun, VERSION 4.0.5<br>&gt;&nbsp; &nbsp; &nbsp; &gt; Source code file: constr.c, line: 136<br>&gt;&nbsp; &nbsp; &nbsp; &gt;<br>&gt;&nbsp; &nbsp; &nbsp; &gt; Fatal error:<br>&gt;&nbsp; &nbsp; &nbsp; &gt; Too many LINCS
 warnings (1966)<br>&gt;&nbsp; &nbsp; &nbsp; &gt; If you know what you are doing you can adjust the lincs warning<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;threshold in your mdp file<br>&gt;&nbsp; &nbsp; &nbsp; &gt; or set the environment variable GMX_MAXCONSTRWARN to -1,<br>&gt;&nbsp; &nbsp; &nbsp; &gt; but normally it is better to fix the problem<br>&gt;&nbsp; &nbsp; &nbsp; &gt;&nbsp; i cant understand how to fix the problem.. where actually lies<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;the error? is it in the mdp file i am using? some suggestions will<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;be really helpful in this regard. Thank you all for the help in advance.<br>&gt; <br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;<a href="http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings</a><br>&gt; <br>&gt; <br>&gt; <br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Thanks You Mark. for your help...
 perhaps the error lies lies in EM<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;step which converged very early in previous steps. when i was<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;running EM for 5000 steps it was converging in less than 50 steps.<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;and was showing a msg like<br>&gt; <br>&gt; <br>&gt;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp;Stepsize too small, or no change in energy. Converged to machine<br>&gt;&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp;precision, but not to the requested precision<br>&gt; <br>&gt; <br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;would doule precision remove this problem? again i cant rule out the<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;system blowing up error. in that case how to increase 1-4 interaction?<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;looking forward for your valuable comments. Thank You<br>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Shamik<br>&gt; <br><br>The question is not when energy minimization converged, but whether or not it converged to an
 appropriate value of Epot and Fmax.&nbsp; What values did you obtain?<br><br>-Justin<br><br>hi, Justin..good to hear from you again...<br>the values i got are given below (taken from the log file):<br><br><font style="color: rgb(82, 83, 48);" size="3"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">Stepsize too small, or no change in energy.</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">Converged to machine precision,</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">but not to the requested precision Fmax &lt; 1000</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new
 york,times,serif; font-weight: bold;">Double precision normally gives you higher accuracy.</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">You might need to increase your constraint accuracy, or turn</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">off constraints alltogether (set constraints = none in mdp file)</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">Steepest Descents converged to machine precision in 31 steps,</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif;
 font-weight: bold;">but did not reach the requested Fmax &lt; 1000.</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">Potential Energy&nbsp; = -1.0261834e+23</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">Maximum force&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 4.9815813e+24 on atom 169274</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">Norm of force&nbsp;&nbsp;&nbsp;&nbsp; =&nbsp; 6.4473938e+21</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight:
 bold;">&nbsp;&nbsp;&nbsp; M E G A - F L O P S&nbsp;&nbsp; A C C O U N T I N G</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;&nbsp; RF=Reaction-Field&nbsp; FE=Free Energy&nbsp; SCFE=Soft-Core/Free Energy</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;&nbsp; T=Tabulated&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; W3=SPC/TIP3p&nbsp;&nbsp;&nbsp; W4=TIP4p (single or pairs)</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;&nbsp; NF=No Forces</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br style="font-family:
 garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Computing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M-Number&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M-Flops&nbsp; % Flops</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">-----------------------------------------------------------------------</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;LJ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 30.494607&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1006.322&nbsp;&nbsp;&nbsp;&nbsp; 0.1</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Coul(T)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 24.286588&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1020.037&nbsp;&nbsp;&nbsp;&nbsp; 0.1</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Coul(T) [W3]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0..205871&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 25.734&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new
 york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Coul(T) + LJ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13.019726&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 716.085&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Coul(T) + LJ [W3]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.396028&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1158.652&nbsp;&nbsp;&nbsp;&nbsp; 0.1</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Coul(T) + LJ
 [W3-W3]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3018.437056&nbsp;&nbsp;&nbsp;&nbsp; 1153042.955&nbsp;&nbsp;&nbsp; 71.1</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Outer nonbonded loop&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 318.129558&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3181.296&nbsp;&nbsp;&nbsp;&nbsp; 0.2</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;1,4 nonbonded interactions&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.204724&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 18.425&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif;
 font-weight: bold;">&nbsp;Calc Weights&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 229.781517&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8272.135&nbsp;&nbsp;&nbsp;&nbsp; 0.5</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Spread Q Bspline&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4902.005696&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9804.011&nbsp;&nbsp;&nbsp;&nbsp; 0.6</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Gather F Bspline&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4902.005696&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 58824.068&nbsp;&nbsp;&nbsp;&nbsp;
 3.6</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;3D-FFT&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 21969.184718&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 175753.478&nbsp;&nbsp;&nbsp; 10.8</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Solve PME&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 234.707200&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15021.261&nbsp;&nbsp;&nbsp;&nbsp; 0.9</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight:
 bold;">&nbsp;NS-Pairs&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8380.302391&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 175986.350&nbsp;&nbsp;&nbsp; 10.8</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Reset In Box&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 25.604636&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 76.814&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Shift-X&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 76.593746&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 459.562&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;CG-CoM&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 76.593839&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 229.782&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Bonds&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.247597&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.608&nbsp;&nbsp;&nbsp;&nbsp;
 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Angles&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.306280&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 51.455&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Propers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.117800&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 26.976&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span
 style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Impropers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.043276&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.001&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;RB-Dihedrals&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.092256&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 22.787&nbsp;&nbsp;&nbsp;&nbsp; 0.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight:
 bold;">&nbsp;Virial&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 76.595234&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1378.714&nbsp;&nbsp;&nbsp;&nbsp; 0.1</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Settle&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 50.895614&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 16439.283&nbsp;&nbsp;&nbsp;&nbsp; 1.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">-----------------------------------------------------------------------</span><br style="font-family: garamond,new
 york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Total&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1622539.792&nbsp;&nbsp; 100.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">-----------------------------------------------------------------------</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight:
 bold;">&nbsp;&nbsp;&nbsp;&nbsp; R E A L&nbsp;&nbsp; C Y C L E&nbsp;&nbsp; A N D&nbsp;&nbsp; T I M E&nbsp;&nbsp; A C C O U N T I N G</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Computing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Nodes&nbsp;&nbsp;&nbsp;&nbsp; Number&nbsp;&nbsp;&nbsp;&nbsp; G-Cycles&nbsp;&nbsp;&nbsp; Seconds&nbsp;&nbsp;&nbsp;&nbsp; %</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">-----------------------------------------------------------------------</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Neighbor
 search&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 31&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 640.014&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 240.7&nbsp;&nbsp;&nbsp; 37.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Force&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 31&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 731.948&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 275..2&nbsp;&nbsp;&nbsp; 42.3</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;PME mesh&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 31&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 308.593&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 116.0&nbsp;&nbsp;&nbsp; 17.8</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Constraints&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 61&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 24.854&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.3&nbsp;&nbsp;&nbsp;&nbsp; 1.4</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Rest&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 25.920&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.7&nbsp;&nbsp;&nbsp;&nbsp; 1.5</span><br
 style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">-----------------------------------------------------------------------</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;Total&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1731.330&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 651.0&nbsp;&nbsp; 100.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">-----------------------------------------------------------------------</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br
 style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;&nbsp;&nbsp; Parallel run - timing based on wallclock.</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; NODE (s)&nbsp;&nbsp; Real (s)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (%)</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Time:&nbsp;&nbsp;&nbsp; 651.000&nbsp;&nbsp;&nbsp; 651.000&nbsp;&nbsp;&nbsp; 100.0</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span
 style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 10:51</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (Mnbf/s)&nbsp;&nbsp; (GFlops)&nbsp;&nbsp; (steps/hour)</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">Performance:&nbsp;&nbsp;&nbsp;&nbsp; 41.873&nbsp;&nbsp; 1622.540&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 171.4</span><br style="font-family: garamond,new york,times,serif; font-weight: bold;"><span style="font-family: garamond,new york,times,serif; font-weight: bold;">Finished mdrun on
 node 0 Wed Jul 15 14:03:57 2009</span><br style="font-family: garamond,new york,times,serif;"></font><br><br>it took just 30 steps to converge... waiting for your answar..<br>Thank You <br>Shamik<br></div></blockquote></td></tr></table><br>
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