The energies simply do not seem to come down any further within several thousand steps.
I start with a .mol2 file which contains the structure of ethylene glycol (ethanediol). These are the commands that I use to set up and run the minimisation: $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 the above command outputs the following files: ethanediol.gro ethanediol.log ethanediolMOL.mol2 ethanediol.top ffethanediol.itp posreethanediol.itp I then proceed to enlarge the box and solvate the molecule: $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5 $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p ethanediol.top -shell 1 I then use grompp to configure the minimisation: $ grompp -f minim.mdp -c ethanediol_box.gro -p ethanediol.top -o em.tpr This is my .mdp file for minimisation: =============================== define = -DPOSRE integrator = steep emtol = 10.0 emstep = 0.01 nsteps = 2000 nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 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 =============================== $ mdrun -v -deffnm em the minimisation runs without error and these are the last few lines of output: =========================================== Step= 1990, Dmax= 1.1e-05 nm, Epot= -1.76427e+04 Fmax= 1.25524e+04, atom= 304 Step= 1991, Dmax= 1.3e-05 nm, Epot= -1.76433e+04 Fmax= 3.13881e+04, atom= 484 Step= 1992, Dmax= 1.6e-05 nm, Epot= -1.76443e+04 Fmax= 2.11785e+04, atom= 484 Step= 1993, Dmax= 1.9e-05 nm, Epot= -1.76445e+04 Fmax= 4.22489e+04, atom= 484 Step= 1994, Dmax= 2.3e-05 nm, Epot= -1.76456e+04 Fmax= 3.33021e+04, atom= 484 Step= 1996, Dmax= 1.4e-05 nm, Epot= -1.76468e+04 Fmax= 1.26110e+04, atom= 304 Step= 1997, Dmax= 1.6e-05 nm, Epot= -1.76474e+04 Fmax= 3.81619e+04, atom= 484 Step= 1998, Dmax= 2.0e-05 nm, Epot= -1.76486e+04 Fmax= 2.68240e+04, atom= 484 Step= 2000, Dmax= 1.2e-05 nm, Epot= -1.76496e+04 Fmax= 1.26501e+04, atom= 304 writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 2001 steps. Potential Energy = -1.7649566e+04 Maximum force = 1.2650057e+04 on atom 30 Norm of force = 1.7544460e+03 =========================================== If I proceed to equilibration after doing the above, the water molecules simply fly apart (although not immediately). Additionally, it seems that there are no interactions between the waters during equilibration. I have tried to run the minimisation for a larger number of steps, but it does not help. I have also tried to delete individual water molecules from the structure files, but doing so simply causes the minimisation to "fixate" on another two molecules. I am not sure what values of the energies are reasonable for this system, and how to minimise it further. Please advise. Thank you. Nancy On Thu, Aug 6, 2009 at 8:38 AM, Bruce D. Ray <bruced...@yahoo.com> wrote: > On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy <nancy5vi...@gmail.com> > wrote: > > I am trying to run equilibration on my solvated ethylene glycol > (ethanediol) system. I started > > with an ethanediol mol2 file from which topolbuild generated various > files. I used editconf > > to enlarge to box of the "ethanediol.gro" file: > > > > $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5 > > > > and then I used genbox to solvate it: > > > > $ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o > ethanediol_solv.gro -p ethanediol.top > > > > I ran energy minimisation on it: > > > > $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr > > > > my minim.mdp file is: > > > > ========================== > > define = -DFLEXIBLE > > integrator = steep > > emtol = 1000.0 > > emstep = 0.01 > > nsteps = 5000 > > > > nstlist = 1 > > ns_type = grid > > rlist = 1.0 > > coulombtype = PME > > rcoulomb = 1.0 > > rvdw = 1.3 > > pbc = xyz > > > > pme_order = 4 > > constraints = none > > > > nstxout = 1 > > nstvout = 1 > > nstenergy = 1 > > nstlog = 1 > > ========================== > > > > $ mdrun -v -deffnm em > > > > and the energies converge (although I think that the values are still too > large for this system): > > > > ========================== > > Steepest Descents converged to Fmax < 1000 in 12 steps > > Potential Energy = -1.1206108e+04 > > Maximum force = 9.4016180e+02 on atom 31 > > Norm of force = 3.4989252e+02 > > ========================== > > {remainder snipped} > > The energies do seem large. What happens if you do energy minimization > with emtol = 10.0 ? > > > -- > Bruce D. Ray, Ph.D. > Associate Scientist, and Operations Director > NMR Center > IUPUI > Physics Dept. > 402 N. Blackford St. > Indianapolis, IN 46202-3273 > > > *From:* Nancy <nancy5vi...@gmail.com> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org> > *Sent:* Wednesday, August 5, 2009 10:28:47 PM > *Subject:* [gmx-users] Energy Minimisation and Equilibration Problems > > > > _______________________________________________ > 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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