[gmx-users] Energy Minimization problem

[George Abadir]

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
> phone: +46 18 471 4537 fax: +46 18 511 755
> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se> 
> http://xray.bmc.uu.se/molbiophys
>
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