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. Please advise Thanks Nancy
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