Thanks guys for your replies. The problem is that the potential energy
is "too" low: it can't be true I think. Also, the high force means that
the system is not really stable (at least the atom influenced by this
force is not!). And yes I defined flexible for the water molecules.
I don't know if there is another solution other than deleting the atom
influenced by the large force, because if I delete it I'll be changing
my system which I would rather not do.
Any help is much appreciated,
Thanks alot,
George
Erik Marklund wrote:
19 apr 2007 kl. 03.45 skrev Venky Krishna:
Hi George,
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?
Best
Venky
On Apr 18, 2007, at 5:24 PM, George Abadir wrote:
Hi,
I am doing an energy minimization for a carbon nanotube (end
capped with hydrogen atoms) in a box of water. I get the following
message:
" 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?
I wouldn't call this an error. The minimization converged, and your
potential energy is low. There is no problem to solve.
/Erik
Thank you very much in advance,
George Abadir
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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