[gmx-users] some problems when using g_membed

[Mark Abraham]

On 18/10/2011 2:08 PM, mircial at sjtu.edu.cn wrote:
> Dear All:
>
> I am using g_membed command to insert a protein into a membrane
> bilayer, however, when I run the following command:
>
> g_membed -f input.tpr -p topology.top -xyinit 0.1 -xyend 1.0 -nxy 1000
>
> I encountered the following errors:
>
> Program g_membed, VERSION 4.5.4
> Source code file: constr.c, line: 176
>
> Fatal error:
> Too many LINCS warnings (3270)
> 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
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> Does this mean that there is some un-reasonable physical positions?
> How can I set the environment variable GMX_MAXCONSTRWARN to -1 or how
> can I avoid this error?

g_membed is a modified version of mdrun. As such, see
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Mark