[gmx-users] Energy minimization Error

francesca vitalini francesca.vitalini11 at gmail.com
Thu Feb 9 19:06:58 CET 2012


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?

2012/2/9 Justin A. Lemkul <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>
>
> -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>
>> >
>> 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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