Hello, 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 ========================== When I try to run equilibration with the following .mdp file: ========================== title = Ethanediol equilibration define = -DPOSRES integrator = md nsteps = 5000 dt = 0.0002 nstxout = 10 nstvout = 10 nstenergy = 10 nstlog = 10 continuation = no constraint_algorithm = lincs constraints = all-angles lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.3 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = EDO SOL tau_t = 0.1 0.1 ref_t = 300 300 pcoupl = no pbc = xyz DispCorr = EnerPres gen_vel = yes gen_temp = 300 gen_seed = -1 ========================== the system "blows up". Addtionally, the structure of the solute is incorrect (all atoms are bonded to each other). Please advise on how to minimise such a system further, and as to why the equilibration is so unstable. Thank you. Nancy
_______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
