[gmx-users] energy minimization output

[Erik Marklund]

It seems that your input structure has too severe clashes for energy minimization, that there are problems with your topology, or that your mdp options are not adequate. One possible solution, if your topology is correct, is to first perform an energy minimization using soft-core potentials to get rid of some of the structural strain. In any case you should inspect your structure closely, in particular near atom 518.

Erik

26 sep 2012 kl. 10.23 skrev Archana Sonawani:

> Dear Erik,
> 
> I also encountered similar problem. So you mean it cannot be further energy
> minimized? How can we proceed with NPT if the system is not in equilibrium?
> 
> On Wed, Sep 26, 2012 at 1:11 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 
>> 
>> 26 sep 2012 kl. 08.16 skrev Shima Arasteh:
>> 
>>> Dear all,
>>> 
>>> My system contains lipids, protein and water.
>>> I want to energy minimize it, so ran grompp:
>>> 
>>> 
>>> # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
>>> 
>>> and then:
>>> # mdrun -v -deffnm em
>>> 
>>> 
>>> The output is:
>>> Steepest Descents:
>>>   Tolerance (Fmax)   =  1.00000e+03
>>>   Number of steps    =        50000
>>> Step=   14, Dmax= 1.2e-06 nm, Epot=  2.30004e+17 Fmax=         inf,
>> atom= 518
>>> Stepsize too small, or no change in energy.
>>> Converged to machine precision,
>>> but not to the requested precision Fmax < 1000
>>> 
>>> Double precision normally gives you higher accuracy.
>>> You might need to increase your constraint accuracy, or turn
>>> off constraints alltogether (set constraints = none in mdp file)
>>> 
>>> writing lowest energy coordinates.
>>> 
>>> Back Off! I just backed up em.gro to ./#em.gro.3#
>>> 
>>> Steepest Descents converged to machine precision in 15 steps,
>>> but did not reach the requested Fmax < 1000.
>>> Potential Energy  =  2.3000388e+17
>>> Maximum force     =            inf on atom 518
>>> Norm of force     =            inf
>>> 
>>> 
>>> Why the maximum force and norm of it is not written? I repeated it for a
>> few times, but no difference.
>>> 
>>> 
>> 
>> It's written. Unfortunately it's infinite.
>> 
>>> 
>>> Thanks for your suggestions in advance.
>>> Sincerely,
>>> Shima
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>> 
>> -----------------------------------------------
>> Erik Marklund, PhD
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>> phone:    +46 18 471 6688        fax: +46 18 511 755
>> erikm at xray.bmc.uu.se
>> http://www2.icm.uu.se/molbio/elflab/index.html
>> 
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> 
> 
> 
> -- 
> Archana Sonawani-Jagtap
> Junior Research Fellow,
> Biomedical Informatics Centre,
> NIRRH (ICMR), Parel
> Mumbai, India.
> 9960791339
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html