I ran the minimisation, and mdrun gave the following last few lines of output:
================================== Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395 Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395 Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom= 2395 Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom= 2395 Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom= 2395 Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom= 2395 Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom= 2395 Step=19999, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom= 2395 Step=20000, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom= 2395 writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 20001 steps. Potential Energy = -7.1493609e+04 Maximum force = 2.4185994e+04 on atom 2395 Norm of force = 8.1511212e+02 ================================== As you can be seen, the forces still do not converge to Fmax < 10, even after 20,000 steps. Does anyone know what the problem might be? Thanks, Nancy On Thu, Aug 6, 2009 at 6:48 PM, Bruce D. Ray <bruced...@yahoo.com> wrote: > On Thursday, August 6, 2009 at 4:08:18 PM, Nancy <nancy5vi...@gmail.com> > wrote: > > > I have attempted to perform energy minimisation from scratch again, and > these are the > > commands that I am using to do so: > > > > $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir > .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 > > > > which generates the files: > > > > ethanediol.gro > > ethanediol.log > > ethanediolMOL.mol2 > > ethanediol.top > > ffethanediol.itp > > posreethanediol.itp > > > > in the "ethanediol.log" file I noticed the following lines with > asterisks: > > > > ======================================== > > Angles Force Field Results > > Angle Atoms force angle method measured > > 1 H12- C1- H11 ****** ****** ****** 109.403 > > 2 C2- C1- H11 ****** ****** ****** 109.456 > > 3 O1- C1- H11 ****** ****** ****** 109.438 > > 4 C2- C1- H12 ****** ****** ****** 109.537 > > 5 O1- C1- H12 ****** ****** ****** 109.468 > > 6 O1- C1- C2 320.0 109.50 1 109.526 > > 7 C1- C2- O2 320.0 109.50 1 109.526 > > 8 C1- C2- H22 ****** ****** ****** 109.453 > > 9 C1- C2- H21 ****** ****** ****** 109.537 > > 10 H22- C2- O2 ****** ****** ****** 109.439 > > 11 H21- C2- O2 ****** ****** ****** 109.468 > > 12 C2- O2- HO2 450.0 109.50 1 106.864 > > 13 H21- C2- H22 ****** ****** ****** 109.404 > > 14 C1- O1- HO1 450.0 109.50 1 106.864 > > ======================================== > > These are fine. Only the nonpolar hydrogens lack parameters and they are > removed from > consideration in the final topology because this is a united atoms model > force field. > > > I then enlarge the box and solvate the molecule: > > > > $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 3 3 3 -c > > > > $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p > ethanediol.top -box 3 3 3 > > > > There are 2679 atoms (891 waters and 1 ethanediol). I then configure the > minimisation with grompp: > > > > $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr > > > > using the following .mdp file: > > > > ======================================== > > define = -DFLEXIBLE > > Just out of curiosity, why are you defining flexible waters at this point? > > > > integrator = steep > > emtol = 10.0 > > emstep = 0.1 > > nsteps = 15000 > > > > nstlist = 1 > > ns_type = grid > > rlist = 1.0 > > coulombtype = PME > > rcoulomb_switch = 1.0 > > rvdw_switch = 1.3 > > pbc = xyz > > > > pme_order = 4 > > constraints = none > > > > nstxout = 1 > > nstvout = 1 > > nstenergy = 1 > > nstlog = 1 > > nstcomm = 1 > > Tcoupl = no > > Pcoupl = no > > gen_vel = no > > ======================================== > > > > I then run the simulation for 15,000 steps: > > > > $ mdrun -v -deffnm em > > > > the last few lines of output are as follows: > > > > ======================================== > > Step=14991, Dmax= 5.3e-06 nm, Epot= -6.24538e+04 Fmax= 2.50258e+04, atom= > 2397 > > Step=14992, Dmax= 6.4e-06 nm, Epot= -6.24539e+04 Fmax= 3.52982e+04, atom= > 1171 > > Step=14993, Dmax= 7.6e-06 nm, Epot= -6.24540e+04 Fmax= 3.71731e+04, atom= > 2397 > > Step=14994, Dmax= 9.2e-06 nm, Epot= -6.24540e+04 Fmax= 4.93409e+04, atom= > 1171 > > Step=14995, Dmax= 1.1e-05 nm, Epot= -6.24541e+04 Fmax= 5.53109e+04, atom= > 2397 > > Step=14997, Dmax= 6.6e-06 nm, Epot= -6.24546e+04 Fmax= 8.50832e+03, atom= > 1171 > > Step=14998, Dmax= 7.9e-06 nm, Epot= -6.24547e+04 Fmax= 6.37691e+04, atom= > 2397 > > Step=14999, Dmax= 9.5e-06 nm, Epot= -6.24553e+04 Fmax= 2.67488e+04, atom= > 1171 > > Step=15000, Dmax= 1.1e-05 nm, Epot= -6.24548e+04 Fmax= 8.09451e+04, atom= > 2397 > > writing lowest energy coordinates. > > > > Steepest Descents did not converge to Fmax < 10 in 15001 steps. > > Potential Energy = -6.2455254e+04 > > Maximum force = 2.6748828e+04 on atom 1171 > > Norm of force = 9.5851715e+02 > > ======================================== > > > > After viewing the trajectory with ngmx, I noticed that most of the motion > of the water > > molecules occurs within the first 50 picoseconds. > > > > Please advise on how to further minimise this system. > > > I downloaded NSC93876 ethylene glycol as a Sybyl (.sy2) file from NCI, > processed it with > dos2unix, added the missing@<TRIPOS> last line, and named it > ethylene_glycol.mol2 > Charge information is absent on this file as downloaded, and I did not do > anything to > account for charges. This may make my results less than useful. I then > ran the following commands: > > /usr/bdray/bin/topolbuild1_3 -dir /usr/bdray/tables -ff gmx53a6 -n > glycol/ethylene_glycol > editconf -f ethylene_glycol.gro -o ethanediol_box.gro -box 3 3 3 -c > genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p > ethanediol.top -box 3 3 3 > grompp -f em.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr > > File em.mdp includes: > constraints = none > integrator = steep > nsteps = 20000 > ; > ; Energy minimizing stuff > ; > emtol = 10.0 > emstep = 0.01 > > nstlist = 1 > coulombtype = PME > nstcomm = 1 > ns_type = grid > rlist = 1 > rcoulomb = 1.0 > rvdw = 1.3 > nstxout = 1 > pbc = xyz > pme_order = 4 > > I deliberately did not use the flexible waters model with this energy > minimization > I then ran > > mdrun -v -deffnm em > > I got the result: > 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) > > Steepest Descents converged to machine precision in 6291 steps, > but did not reach the requested Fmax < 10. > Potential Energy = -4.9487391e+04 > Maximum force = 9.0675652e+01 on atom 5 > Norm of force = 2.5599347e+02 > > I note that atom 5 is part of the ethylene glycol molecule. Furthermore, > with very few > exceptions, most of the activity in the energy minimization was devoted to > the ethylene > glycol molecule. I presume that I would reach the desired Fmax if I were > to use double > precision. However, an Fmax < 90.7 would seem to me to be usable. > > Perhaps the problem stems from the use of flexible waters in the energy > minimization? > > > -- > Bruce D. Ray, Ph.D. > Associate Scientist > IUPUI > Physics Dept. > 402 N. Blackford St. > Indianapolis, IN 46202-3273 > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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