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
--
========================================
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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