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 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 vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412
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