[gmx-users] Lincs Warning

Samik Bhattacharya samikbhat at yahoo.co.in
Thu Jul 16 03:57:22 CEST 2009

--- 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.


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

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