[gmx-users] Energy minimization Error
francesca vitalini
francesca.vitalini11 at gmail.com
Fri Feb 10 11:28:45 CET 2012
I achieve
Steepest Descents converged to machine precision in 205 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.49131940478719e+07
Maximum force = 1.09664530279637e+06 on atom 1520 (parto of the
protein)
Norm of force = 2.28369808518165e+06
and the system looked with vmd doesn't look as if it was exploding.
However, I have warnings about the table extension and I don't know why but
gromacs writes pdb files sometime. However I thought that there might have
been an error in the way I defined the position restraints, in fact in the
mdp file I hade define = -DEPOSRE while in the topology I had ifdef
DEFINE_WAT, so it might have moved it all without fixing the water. So I
tried again and this time I got
Steepest Descents converged to machine precision in 72 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -2.0135496e+07
Maximum force = 2.0486184e+12 on atom 4479
Norm of force = 7.2424045e+13
but again the same issue with table extent and still the production of pdb
files.
Any explanations?
Thanks
Francesca
2012/2/9 Justin A. Lemkul <jalemkul at vt.edu>
>
>
> francesca vitalini wrote:
>
>> Tryed the double precision without any success... Again the same type of
>> error message. Might need to try other minimization algorithm. Any
>> suggestions on that?
>>
>>
> What is the Fmax you achieve, and what are your intents for this process?
> Minimizing very low is only strictly necessary for certain types of very
> sensitive calculations. For normal MD, convergence below 100-1000
> kJ/mol-nm is typical.
>
> Other algorithms are listed in the manual. They may or may not be
> necessary.
>
> -Justin
>
> 2012/2/9 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>
>>
>>
>> francesca vitalini wrote:
>>
>> Hi all!
>> I'm trying to run some energy minimization with gromacs 3.3.1 on
>> a system that I have transformed from cg to aa. After the
>> reverse transformation I solvate the system and I try to
>> minimize just the proteins (my system is a dimer) keeping fixed
>> the water. Then the idea would be to minimize the water keeping
>> the protein in harmonic distance constraints as I just want to
>> obtain an aa system which describes the configuration obtained
>> previously in the cg representation.
>> So, I first use genrestr to create the .itp file for fixing the
>> position of the water, then I run 10 ps of EM and what I get is
>> the following error 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 alltogether (set constraints = none in mdp file)
>>
>> From what I've read in previous posts the problem might be
>> either in the mdp file or in the topology, but I don't
>> understand what have I made wrong. Here is my mdp file
>>
>>
>> The other possibility is that there is no problem at all. Some
>> systems cannot be minimized below certain thresholds, based on the
>> input geometry. You may also want to try a different minimizer or
>> double precision.
>>
>> http://www.gromacs.org/__**Documentation/Errors#Stepsize_**
>> __too_small.2c_or_no_change_**in___energy._Converged_to_**
>> machine___precision.2c_but_**not_to_the___requested_**precision<http://www.gromacs.org/__Documentation/Errors#Stepsize___too_small.2c_or_no_change_in___energy._Converged_to_machine___precision.2c_but_not_to_the___requested_precision>
>>
>> <http://www.gromacs.org/**Documentation/Errors#Stepsize_**
>> too_small.2c_or_no_change_in_**energy._Converged_to_machine_**
>> precision.2c_but_not_to_the_**requested_precision<http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision>
>> >
>>
>> -Justin
>>
>> Lines starting with ';' ARE COMMENTS
>> ; Everything following ';' is also comment
>>
>> title = Energy Minimization ; Title of run
>>
>> ; The following line tell the program the standard locations
>> where to find certain files
>> cpp = /lib/cpp ; Preprocessor
>>
>> ; Define can be used to control processes
>> define = -DEPOSRES
>> ;define = -DFLEXIBLE
>> ; Parameters describing what to do, when to stop and what to save
>> integrator = steep ; Algorithm (steep = steepest
>> descent minimization)
>> emtol = 10.0 ; Stop minimization when the
>> maximum force < 1.0 kJ/mol
>> dt = 0.005
>> ;nsteps = 2000
>> nsteps = 5000 ; Maximum number of
>> (minimization) steps to perform
>> nstenergy = 1 ; Write energies to disk every
>> nstenergy steps
>> energygrps = System ; Which energy group(s) to write
>> to disk
>>
>> ; Parameters describing how to find the neighbors of each atom
>> and how to calculate the interactions
>> nstlist = 1 ; Frequency to update the
>> neighbor list
>> ns_type = grid ; Method to determine neighbor
>> list (simple, grid)
>> coulombtype = Reaction-Field ; Treatment of long range
>> electrostatic interactions
>> epsilon_rf = 78
>> rcoulomb = 1.4 ; long range electrostatic cut-off
>> rvdw = 1.4 ; long range Van der Waals cut-off
>> constraints = none ; Bond types to replace by
>> constraints
>> pbc = xyz ; Periodic Boundary Conditions
>> (yes/no)
>>
>> table-extension = 1.2
>>
>> and this is my topology
>>
>> ;
>> ; File 'dynamin_dimer_fg.top' was generated
>> ; By user: vitalini (213883)
>> ; On host: goat
>> ; At date: Mon Jan 30 11:02:21 2012
>> ;
>> ; This is your topology file
>> ; "The Poodle Chews It" (F. Zappa)
>> ;
>> ; Include forcefield parameters
>> #include
>> "/home/cocktail/vitalini/__**gromacs_special/share/gromacs/**
>> __top/ffG53a6m.itp"
>>
>>
>> ; Include chain topologies
>> #include "dynamin_dimer_fg_A.itp"
>> #include "dynamin_dimer_fg_B.itp"
>>
>> ; Include water topology
>> #include
>> "/home/cocktail/vitalini/__**gromacs_special/share/gromacs/**
>> __top/spc.itp"
>>
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 1 1 1000 1000 1000
>> #endif
>>
>>
>> ;Include restraints on water
>> #ifdef POSRES_WAT
>> #include "posre_wat.itp"
>> #endif
>>
>> ; Include generic topology for ions
>> #include
>> "/home/cocktail/vitalini/__**gromacs_special/share/gromacs/**
>> __top/ions.itp"
>>
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound #mols
>> Protein_A 1
>> Protein_B 1
>> ;SOL 390842
>> SOL 390820
>> NA+ 22
>>
>> while this is the posre_wat.itp file I generated with genrestr
>>
>> ; position restraints for non-Protein of Protein in water
>>
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 15231 1 1000 1000 1000
>> 15232 1 1000 1000 1000
>> 15233 1 1000 1000 1000
>> 15234 1 1000 1000 1000
>> 15235 1 1000 1000 1000
>> 15236 1 1000 1000 1000
>> 15237 1 1000 1000 1000
>> 15238 1 1000 1000 1000
>> 15239 1 1000 1000 1000
>> 15240 1 1000 1000 1000
>> 15241 1 1000 1000 1000
>> 15242 1 1000 1000 1000
>> 15243 1 1000 1000 1000
>> 15244 1 1000 1000 1000
>> 15245 1 1000 1000 1000
>> 15246 1 1000 1000 1000
>> 15247 1 1000 1000 1000
>> 15248 1 1000 1000 1000
>> 15249 1 1000 1000 1000
>> 15250 1 1000 1000 1000
>> 15251 1 1000 1000 1000
>> ..........................
>> 187712 1 1000 1000 1000
>>
>> Any help?
>> Thanks Francesca
>>
>>
>> -- Francesca Vitalini
>>
>> PhD student at Computational Molecular Biology Group,
>> Department of Mathematics and Informatics, FU-Berlin
>> Arnimallee 6 14195 Berlin
>>
>> vitalini at zedat.fu-berlin.de <mailto:vitalini at zedat.fu-**berlin.de<vitalini at zedat.fu-berlin.de>
>> >
>> <mailto:vitalini at zedat.fu-__**berlin.de<vitalini at zedat.fu-__berlin.de>
>> <mailto:vitalini at zedat.fu-**berlin.de<vitalini at zedat.fu-berlin.de>
>> >>
>> francesca.vitalini at fu-berlin._**_de
>> <mailto:francesca.vitalini at fu-**berlin.de<francesca.vitalini at fu-berlin.de>
>> >
>> <mailto:francesca.vitalini at fu-**__berlin.de<francesca.vitalini at fu-__berlin.de>
>> <mailto:francesca.vitalini at fu-**berlin.de<francesca.vitalini at fu-berlin.de>
>> >>
>>
>> +49 3083875776 <tel:%2B49%203083875776>
>> +49 3083875412 <tel:%2B49%203083875412>
>>
>>
>> -- ==============================**__==========
>>
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> <tel:%28540%29%20231-9080>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>> ==============================**__==========
>>
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>>
>>
>> --
>> Francesca Vitalini
>>
>> PhD student at Computational Molecular Biology Group,
>> Department of Mathematics and Informatics, FU-Berlin
>> Arnimallee 6 14195 Berlin
>>
>> vitalini at zedat.fu-berlin.de <mailto:vitalini at zedat.fu-**berlin.de<vitalini at zedat.fu-berlin.de>
>> >
>> francesca.vitalini at fu-berlin.**de <francesca.vitalini at fu-berlin.de><mailto:
>> francesca.vitalini at fu-**berlin.de <francesca.vitalini at fu-berlin.de>>
>>
>> +49 3083875776
>> +49 3083875412
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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--
Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de
+49 3083875776
+49 3083875412
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