I tried decreasing emstep, and also tried increasing the number of steps, but I still get the following output from mdrun:
================================================== Steepest Descents did not converge to Fmax < 1000 in 5001 steps. Potential Energy = -6.9329155e+03 Maximum force = 2.1965221e+04 on atom 39 Norm of force = 2.1487129e+03 ================================================== Please advise on how to further decrease the forces. Thanks, Nancy On Wed, Aug 5, 2009 at 6:08 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Nancy wrote: > >> Hello, >> >> 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 >> >> 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 think this is the root of your problem. The maximum force is far too > high. Decrease your value of emstep (the default of 0.01 is generally fine), > and try again. You will not likely see large changes over the course of the > trajectory. EM makes small changes to optimize geometry, hydrogen bonding, > etc. There are no dynamics (remember that EM is essentially conducted at 0 > K). > > -Justin > > Please advise >> >> Thanks >> >> Nancy >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > 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 > 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 >
_______________________________________________ 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
