[gmx-users] Lincs Warning

[Justin A. Lemkul]

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

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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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