Dear Justin,
Thank you for your answer. Regarding the message below:
1- How is it possible to have a reasonable max force but not a resonable
potential?
2- To remove this high potential from system, What do you suggest?
2-1 Do I need to reduce the number of molecules in the box (reduce
density?)
2-2 Dies the idea of changinf cut off radius (you mentioned somewhere
inthe archive) would work?
3- How Can I view the potential energies arising form various contributions?
(electrostatics, vdw,..) to see which type is causing problem?
Thank you for your help.
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.
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