[email protected] wrote:
<snip>
Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.7206969e+04
Maximum force = 2.0111207e+04 on atom 1217
Norm of force = 6.9283209e+02
I don't understand constraints I need to turn off, since I haven't
mentioned any in my grompp file.
This is just generic advice that mdrun provides. The fact is your starting
structure contains atomic overlap or clashes that cannot be resolved by energy
minimization. Have a look at the trajectory and see if you can get some insight
into where things are going wrong (since problematic atom numbers are being
printed, and perhaps re-consider how you built your system.
-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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