[gmx-users] Lincs warning

[Justin A. Lemkul]

Moeed wrote:
> 
> Dear gmx experts,
> 
> I am having problem doing MD run for a hydrocarbon system. The system 
> contains a stack of Hexane molecules using editconf. 
> 
> The distance between molecuels in the box is more than 30 A. I am 
> wondering why I get large forces (system is blowing up) with this 
> distance!. (LINCS warning) with dt=0.002
> Program mdrun, VERSION 4.0.7
> Source code file: constr.c, line: 136
> 
> Fatal error:
> Too many LINCS warnings (1053)
> 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
> 
> 
> It seems Fmax, Epot values are reasonable. . In the list archive I read 

I would say they are not.

<snip>

> Steepest Descents converged to Fmax < 1000 in 30 steps
> Potential Energy  =  4.76092783832156e+05
> Maximum force     =  9.86600079729483e+02 on atom 3115
> Norm of force     =  5.33725886931530e+02

You have a reasonable force, but your potential energy is large and positive, 
indicative strong repulsive forces in your system.

<snip>

> define              =  -DPOSRES

What are you restraining, and what purpose does it serve?

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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