[gmx-users] Energy Minimization problem
erikm at xray.bmc.uu.se
Thu Apr 19 09:41:04 CEST 2007
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?
> 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?
I wouldn't call this an error. The minimization converged, and your
potential energy is low. There is no problem to solve.
>> 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
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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