On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy <nancy5vi...@gmail.com> wrote: > I was trying to run equilibration on my solvated ethylene glycol system. However, the > system seems to be "exploding". I believe this is due to inadequate energy minimisation, > however, I am unable to minimise my system any further. I am using the following .mdp > file "minim.mdp" for minimsation: > > ============================== > define = -DFLEXIBLE > integrator = steep > emtol = 1000.0 > emstep = 0.5 > nsteps = 1000
I use more steps than 1000 (may want 10000) with: emstep = 0.01 nstcomm = 1 Tcoupl = no Pcoupl = no gen_vel = no > > nstlist = 1 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > rvdw = 1.3 > pbc = xyz > > pme_order = 4 > constraints = none > ============================== > > I process it with grompp, where "ethanediol_solv.gro" is the solvated system, > and "ethanediol.top" is the topolgy generated with topolbuild: > > $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr > > I then run it: > > $ mdrun -v -deffnm em > > mdrun outputs the following information: > > ============================== > Steepest Descents did not converge to Fmax < 1000 in 1001 steps. > Potential Energy = -6.7546914e+03 > Maximum force = 2.7262363e+04 on atom 34 > Norm of force = 2.5032930e+03 > ============================== > > I have viewed the output trajectory of the minimisation and I can see that the > waters do not move much. I am wondering if there is a way to let solvent water > molecules move about during minimsation, and/or how to remove some of them. > I am also unsure what value of emtol is reasonable for this type of small system. I use the same value of emtol, but that's just based on examples I've seen where others have used that value. -- 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 6:03:51 PM >Subject: [gmx-users] Energy Minimisation Values > > >
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