Hello,<br><br>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:<br>
<br>==============================<br>define = -DFLEXIBLE<br>integrator = steep<br>emtol = 1000.0<br>emstep = 0.5<br>nsteps = 1000<br><br>nstlist = 1<br>ns_type = grid<br>rlist = 1.0<br>
coulombtype = PME<br>rcoulomb = 1.0<br>rvdw = 1.3<br>pbc = xyz<br><br>pme_order = 4<br>constraints = none<br>==============================<br><br>I process it with grompp, where "ethanediol_solv.gro" is the solvated system, and "ethanediol.top" is the topolgy generated with topolbuild:<br>
<br>$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr<br><br>I then run it:<br><br>$ mdrun -v -deffnm em<br><br>mdrun outputs the following information:<br><br>==============================<br>Steepest Descents did not converge to Fmax < 1000 in 1001 steps.<br>
Potential Energy = -6.7546914e+03<br>Maximum force = 2.7262363e+04 on atom 34<br>Norm of force = 2.5032930e+03<br>==============================<br><br>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.<br>
<br>Please advise<br><br>Thanks<br><br>Nancy<br><br><br><br>