Dear Justin,<br><br>Thank you for your answer. Regarding the message below:<br><br>1- How is it possible to have a reasonable max force but not a resonable potential?<br>2- To remove this high potential from system, What do you suggest? <br>
2-1 Do I need to reduce the number of molecules in the box (reduce density?)<br> 2-2 Dies the idea of changinf cut off radius (you mentioned somewhere inthe archive) would work? <br>3- How Can I view the potential energies arising form various contributions? (electrostatics, vdw,..) to see which type is causing problem?<br>
<br><br>Thank you for your help.<br><br><br><br>Moeed wrote:<br>
><br>
> Dear gmx experts,<br>
><br>
> I am having problem doing MD run for a hydrocarbon system. The system<br>
> contains a stack of Hexane molecules using editconf.<br>
><br>
> The distance between molecuels in the box is more than 30 A. I am<br>
> wondering why I get large forces (system is blowing up) with this<br>
> distance!. (LINCS warning) with dt=0.002<br>
> Program mdrun, VERSION 4.0.7<br>
> Source code file: constr.c, line: 136<br>
><br>
> Fatal error:<br>
> Too many LINCS warnings (1053)<br>
> If you know what you are doing you can adjust the lincs warning<br>
> threshold in your mdp file<br>
> or set the environment variable GMX_MAXCONSTRWARN to -1,<br>
> but normally it is better to fix the problem<br>
><br>
><br>
> It seems Fmax, Epot values are reasonable. . In the list archive I read<br>
<br>
I would say they are not.<br>
<br>
<snip><br>
<br>
> Steepest Descents converged to Fmax < 1000 in 30 steps<br>
> Potential Energy = 4.76092783832156e+05<br>
> Maximum force = 9.86600079729483e+02 on atom 3115<br>
> Norm of force = 5.33725886931530e+02<br>
<br>
You have a reasonable force, but your potential energy is large and positive,<br>
indicative strong repulsive forces in your system.<br>
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