[gmx-users] Energy Minimization problem

[Erik Marklund]

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	http://xray.bmc.uu.se/molbiophys


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