[gmx-users] about "LINCS WARNING"

[K.A. Feenstra]

zhang ray wrote:
> 
> Thank you Anton Feenstra, Kun-Lin Yang, and all gmx-users
>    And could you please check my control files(in attachment)?
>    I used Gromacs in this flow:
>         1. Constructed my starting coordinates(conf.gro) by a piece of CPP code
> (con_build.cpp)
>         2. ankyl.itp + C10.itp -> topol.top;
>          3. Em.mdp is energy minimize control file;
>         4. Main.mdp is md control file,

You use nstlist=0, rlist=1.0, rvwd=1.0 and rcoulomb=1.0. 
I'd rather set nstlist <= 10 and rvwd and rcooulomb should normally
be set to 1.4 (for the Gromos forcefield, anyway). rlist can be
shorter, 0.85.

Further, I have no idea how your program generates the initial
coordinates (and no intention of finding out), however, it is
quite likely that your problem lies there. Check out the separate
energy terms (e.g. angles, Lennard-Jones, etc.) to see which
ones might be unnaturally high. Also, gmxcheck -c on your .gro
file will tell you something about overlapping atoms.

Finally, your alkyl.itp contains a [nonbond_params] section, and
another [nonbond_params] section is inside the ffgmx*.itp files.
IIRC, this does not work as expected and both sections should be
merged. Search the list for how to do it (it is described for 
merging lipid.itp into ffgmx*.itp). It is unlikely, however, that 
this would explain your problems.



-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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