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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.<br>
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.<br>
Any help is much appreciated,<br>
Thanks alot,<br>
George<br>
<br>
<br>
Erik Marklund wrote:
<blockquote
cite="mid53D6EA14-BD30-454F-9879-274A27F26748@xray.bmc.uu.se"
type="cite"><br>
<div>
<div>19 apr 2007 kl. 03.45 skrev Venky Krishna:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Hi George,
<div><br class="khtml-block-placeholder">
</div>
<div>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?</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Best</div>
<div>Venky</div>
<div><br>
<div>
<div>On Apr 18, 2007, at 5:24 PM, George Abadir wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"> Hi,<br>
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:<br>
<font color="#3333ff">" Stepsize too small, or no change in
energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 10<br>
<br>
Double precision normally gives you higher accuracy.<br>
You might need to increase your constraint accuracy, or turn off
constraints altogether (set constraints = none in mdp file)<br>
<br>
Steepest Descents converged to machine precision in 1836 steps, but did
not reach the requested Fmax < 10.<br>
Potential Energy = -2.4277438+06<br>
Maximum force = 5.9858018+03 on atom 13<br>
Norm of force = 5.1364398+04"</font><br>
<br>
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?<br>
<br>
</blockquote>
</div>
</div>
</blockquote>
<br>
I wouldn't call this an error. The minimization converged, and your
potential energy is low. There is no problem to solve.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>/Erik</div>
<div><br>
<blockquote type="cite">
<div>
<div>
<blockquote type="cite"> Thank you very much in advance,<br>
George Abadir<br>
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<div>_______________________________________________</div>
<div>Erik Marklund, PhD student</div>
<div>Laboratory of Molecular Biophysics,</div>
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