[gmx-users] Lincs Warning
Samik Bhattacharya
samikbhat at yahoo.co.in
Thu Jul 16 06:13:30 CEST 2009
--- On Thu, 16/7/09, Justin A. Lemkul <jalemkul at vt.edu> wrote:
From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Lincs Warning
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thursday, 16 July, 2009, 7:30 AM
Samik Bhattacharya wrote:
>
>
> --- On *Wed, 15/7/09, Mark Abraham /<Mark.Abraham at anu.edu.au>/* wrote:
>
>
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Lincs Warning
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Wednesday, 15 July, 2009, 5:23 PM
>
> Samik Bhattacharya wrote:
> > Hi all, i ma simulating a membrane protein, in which i am facing
> a problem in the equilibration step. in the NVT equilibration when i
> am running the mdrun command i am getting a msg like
> >
> > Program mdrun, VERSION 4.0.5
> > Source code file: constr.c, line: 136
> >
> > Fatal error:
> > Too many LINCS warnings (1966)
> > If you know what you are doing you can adjust the lincs warning
> threshold in your mdp file
> > or set the environment variable GMX_MAXCONSTRWARN to -1,
> > but normally it is better to fix the problem
> > i cant understand how to fix the problem.. where actually lies
> the error? is it in the mdp file i am using? some suggestions will
> be really helpful in this regard. Thank you all for the help in advance.
>
> http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
>
>
>
> Thanks You Mark. for your help... perhaps the error lies lies in EM
> step which converged very early in previous steps. when i was
> running EM for 5000 steps it was converging in less than 50 steps.
> and was showing a msg like
>
>
> Stepsize too small, or no change in energy. Converged to machine
> precision, but not to the requested precision
>
>
> would doule precision remove this problem? again i cant rule out the
> system blowing up error. in that case how to increase 1-4 interaction?
> looking forward for your valuable comments. Thank You
> Shamik
>
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?
-Justin
hi, Justin..good to hear from you again...
the values i got are given below (taken from the log file):
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Steepest Descents converged to machine precision in 31 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -1.0261834e+23
Maximum force = 4.9815813e+24 on atom 169274
Norm of force = 6.4473938e+21
M E G A - F L O P S A C C O U N T I N G
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------
LJ 30.494607 1006.322 0.1
Coul(T) 24.286588 1020.037 0.1
Coul(T) [W3] 0.205871 25.734 0.0
Coul(T) + LJ 13.019726 716.085 0.0
Coul(T) + LJ [W3] 8.396028 1158.652 0.1
Coul(T) + LJ [W3-W3] 3018.437056 1153042.955 71.1
Outer nonbonded loop 318.129558 3181.296 0.2
1,4 nonbonded interactions 0.204724 18.425 0.0
Calc Weights 229.781517 8272.135 0.5
Spread Q Bspline 4902.005696 9804.011 0.6
Gather F Bspline 4902.005696 58824.068 3.6
3D-FFT 21969.184718 175753.478 10.8
Solve PME 234.707200 15021.261 0.9
NS-Pairs 8380.302391 175986.350 10.8
Reset In Box 25.604636 76.814 0.0
Shift-X 76.593746 459.562 0.0
CG-CoM 76.593839 229.782 0.0
Bonds 0.247597 14.608 0.0
Angles 0.306280 51.455 0..0
Propers 0.117800 26.976 0..0
Impropers 0.043276 9.001 0.0
RB-Dihedrals 0.092256 22.787 0.0
Virial 76.595234 1378.714 0.1
Settle 50.895614 16439.283 1.0
-----------------------------------------------------------------------
Total 1622539.792 100.0
-----------------------------------------------------------------------
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
Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Neighbor search 1 31 640.014 240.7 37.0
Force 1 31 731.948 275.2 42.3
PME mesh 1 31 308.593 116.0 17.8
Constraints 1 61 24.854 9.3 1.4
Rest 1 25.920 9.7 1.5
-----------------------------------------------------------------------
Total 1 1731.330 651.0 100.0
-----------------------------------------------------------------------
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 651.000 651.000 100.0
10:51
(Mnbf/s) (GFlops) (steps/hour)
Performance: 41.873 1622.540 171.4
Finished mdrun on node 0 Wed Jul 15 14:03:57 2009
it took just 30 steps to converge... waiting for your answar..
Thank You
Shamik
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