[gmx-users] Energy Minimization problem
venky.agas at gmail.com
Thu Apr 19 03:45:35 CEST 2007
I usually delete/move the molecules reported to have high force
values in the minimization steps. A better thing would be to start
with a box which has sufficient intermolecular distance again by
deleting molecules which are very close to each other (use the
g_mindist program) and then energy minimize the system. Btw...did you
define FLEXIBLE for water molecules during your em runs?
On Apr 18, 2007, at 5:24 PM, George Abadir wrote:
> I am doing an energy minimization for a carbon nanotube (end
> capped with hydrogen atoms) in a box of water. I get the following
> " Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn off
> constraints altogether (set constraints = none in mdp file)
> Steepest Descents converged to machine precision in 1836 steps, but
> did not reach the requested Fmax < 10.
> Potential Energy = -2.4277438+06
> Maximum force = 5.9858018+03 on atom 13
> Norm of force = 5.1364398+04"
> The potential energy is extremely low and the maximum force is
> considerably large. I turned off the constrained and tried other
> energy minimization methods but still got the same error (with
> different magnitudes of the force and energy of course). Is it
> likely that double precision simulation can make such a big
> difference? If not (which I think) is there any other way to solve
> the problem?
> Thank you very much in advance,
> George Abadir
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