<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><jalemkul@vt.edu></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 <jalemkul@vt.edu><br>Subject: Re: [gmx-users] Lincs Warning<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Thursday, 16 July, 2009, 7:30 AM<br><br><div class="plainMail"><br><br>Samik Bhattacharya wrote:<br>> <br>> <br>> --- On *Wed, 15/7/09, Mark Abraham /<<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="/mc/compose?to=Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>/* wrote:<br>> <br>> <br>> From: Mark Abraham <<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="/mc/compose?to=Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>>
Subject: Re: [gmx-users] Lincs Warning<br>> To: "Discussion list for GROMACS users" <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Date: Wednesday, 15 July, 2009, 5:23 PM<br>> <br>> Samik Bhattacharya wrote:<br>> > Hi all, i ma simulating a membrane protein, in which i am facing<br>> a problem in the equilibration step. in the NVT equilibration when i<br>> am running the mdrun command i am getting a msg like<br>> ><br>> > Program mdrun, VERSION 4.0.5<br>> > Source code file: constr.c, line: 136<br>> ><br>> > Fatal error:<br>> > Too many LINCS
warnings (1966)<br>> > If you know what you are doing you can adjust the lincs warning<br>> threshold in your mdp file<br>> > or set the environment variable GMX_MAXCONSTRWARN to -1,<br>> > but normally it is better to fix the problem<br>> > i cant understand how to fix the problem.. where actually lies<br>> the error? is it in the mdp file i am using? some suggestions will<br>> be really helpful in this regard. Thank you all for the help in advance.<br>> <br>> <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>> <br>> <br>> <br>> Thanks You Mark. for your help...
perhaps the error lies lies in EM<br>> step which converged very early in previous steps. when i was<br>> running EM for 5000 steps it was converging in less than 50 steps.<br>> and was showing a msg like<br>> <br>> <br>> Stepsize too small, or no change in energy. Converged to machine<br>> precision, but not to the requested precision<br>> <br>> <br>> would doule precision remove this problem? again i cant rule out the<br>> system blowing up error. in that case how to increase 1-4 interaction?<br>> looking forward for your valuable comments. Thank You<br>> Shamik<br>> <br><br>The question is not when energy minimization converged, but whether or not it converged to an
appropriate value of Epot and Fmax. 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 < 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 < 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 = -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 = 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 = 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;"> M E G A - F L O P S 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;"> RF=Reaction-Field FE=Free Energy 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;"> T=Tabulated W3=SPC/TIP3p 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;"> 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;"> Computing: M-Number M-Flops % 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;"> LJ
30.494607 1006.322 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;"> Coul(T) 24.286588 1020.037 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;"> Coul(T) [W3] 0..205871 25.734 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;"> Coul(T) + LJ 13.019726 716.085 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;"> Coul(T) + LJ [W3] 8.396028 1158.652 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;"> Coul(T) + LJ
[W3-W3] 3018.437056 1153042.955 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;"> Outer nonbonded loop 318.129558 3181.296 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;"> 1,4 nonbonded interactions 0.204724 18.425 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;"> Calc Weights 229.781517 8272.135 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;"> Spread Q Bspline 4902.005696 9804.011 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;"> Gather F Bspline 4902.005696 58824.068
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;"> 3D-FFT 21969.184718 175753.478 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;"> Solve PME 234.707200 15021.261 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;"> NS-Pairs 8380.302391 175986.350 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;"> Reset In Box 25.604636 76.814 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;"> Shift-X
76.593746 459.562 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;"> CG-CoM 76.593839 229.782 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;"> Bonds 0.247597 14.608
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;"> Angles 0.306280 51.455 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;"> Propers 0.117800 26.976 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;"> Impropers 0.043276 9.001 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;"> RB-Dihedrals 0.092256 22.787 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;"> Virial 76.595234 1378.714 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;"> Settle 50.895614 16439.283 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;"> Total 1622539.792 100.0</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;"> R E A L C Y C L E A N D T I M E 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;"> Computing: Nodes Number G-Cycles Seconds %</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;"> Neighbor
search 1 31 640.014 240.7 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;"> Force 1 31 731.948 275..2 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;"> PME mesh 1 31
308.593 116.0 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;"> Constraints 1 61 24.854 9.3 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;"> Rest 1 25.920 9.7 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;"> Total 1 1731.330 651.0 100.0</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;"> 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;"> NODE (s) Real (s) (%)</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;"> Time: 651.000 651.000 100.0</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;"> 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;"> (Mnbf/s) (GFlops) (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: 41.873 1622.540 171.4</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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