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 <jalem...@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 <jalem...@vt.edu <mailto:jalem...@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 >> >> vital...@zedat.fu-berlin.de >> <mailto:vital...@zedat.fu-**berlin.de<vital...@zedat.fu-berlin.de> >> > >> <mailto:vital...@zedat.fu-__**berlin.de<vital...@zedat.fu-__berlin.de> >> <mailto:vital...@zedat.fu-**berlin.de<vital...@zedat.fu-berlin.de> >> >> >> francesca.vitalini@fu-berlin._**_de >> >> <mailto:francesca.vitalini@fu-**berlin.de<francesca.vital...@fu-berlin.de> >> > >> >> <mailto:francesca.vitalini@fu-**__berlin.de<francesca.vitalini@fu-__berlin.de> >> >> <mailto:francesca.vitalini@fu-**berlin.de<francesca.vital...@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> >> > >> >> ==============================**__========== >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>> >> before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> 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 >> <mailto:vital...@zedat.fu-**berlin.de<vital...@zedat.fu-berlin.de> >> > >> francesca.vitalini@fu-berlin.**de <francesca.vital...@fu-berlin.de><mailto: >> francesca.vitalini@fu-**berlin.de <francesca.vital...@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> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- 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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