[gmx-users] unstability of system, lincs problem
x.periole at rug.nl
Thu Apr 29 18:00:34 CEST 2010
On Apr 29, 2010, at 5:47 PM, Moeed wrote:
> 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?
The potential energy in itself should not matter but the high values
you've got indicates
that there is omething funny!
Did you look at the term(s) reponsible for it? g_energy or in the log
> 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
> Thank you for your help.
> Moeed wrote:
> > Dear gmx experts,
> > I am having problem doing MD run for a hydrocarbon system. The
> > 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
> I would say they are not.
> > 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
> indicative strong repulsive forces in your system.
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