[gmx-users] Lincs Warning

[Samik Bhattacharya]

--- 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



      Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090716/a2789e49/attachment.html>