[gmx-users] Energy minimization Error
Justin A. Lemkul
jalemkul at vt.edu
Thu Feb 9 17:41:17 CET 2012
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
-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>
> francesca.vitalini at fu-berlin.de <mailto: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
========================================
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