Hello,<br><br>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:<br>
<br>$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5<br><br>and then I used genbox to solvate it:<br><br>$ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o ethanediol_solv.gro -p ethanediol.top<br><br>
I ran energy minimisation on it:<br><br>$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr<br><br>my minim.mdp file is:<br><br>==========================<br>define = -DFLEXIBLE<br>integrator = steep<br>
emtol = 1000.0<br>emstep = 0.01<br>nsteps = 5000<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>nstxout = 1<br>nstvout = 1<br>nstenergy = 1<br>nstlog = 1<br>==========================<br><br>$ mdrun -v -deffnm em<br><br>and the energies converge (although I think that the values are still too large for this system):<br>
<br>==========================<br>Steepest Descents converged to Fmax < 1000 in 12 steps<br>Potential Energy = -1.1206108e+04<br>Maximum force = 9.4016180e+02 on atom 31<br>Norm of force = 3.4989252e+02<br>==========================<br>
<br>When I try to run equilibration with the following .mdp file:<br><br>==========================<br>title = Ethanediol equilibration<br>define = -DPOSRES<br>integrator = md <br>nsteps = 5000 <br>
dt = 0.0002<br><br>nstxout = 10 <br>nstvout = 10 <br>nstenergy = 10 <br>nstlog = 10 <br><br>continuation = no<br>constraint_algorithm = lincs <br>constraints = all-angles <br>
lincs_iter = 1 <br>lincs_order = 4 <br><br>ns_type = grid<br>nstlist = 5 <br>rlist = 1.0 <br>rcoulomb = 1.0 <br>rvdw = 1.3 <br><br>coulombtype = PME <br>
pme_order = 4 <br>fourierspacing = 0.16 <br><br>tcoupl = V-rescale <br>tc-grps = EDO SOL <br>tau_t = 0.1 0.1 <br>ref_t = 300 300 <br><br>pcoupl = no <br><br>
pbc = xyz <br><br>DispCorr = EnerPres<br><br>gen_vel = yes <br>gen_temp = 300 <br>gen_seed = -1 <br>==========================<br><br>the system "blows up". Addtionally, the structure of the solute is incorrect (all atoms are bonded to each other).<br>
<br>Please advise on how to minimise such a system further, and as to why the equilibration is so unstable.<br><br>Thank you.<br><br>Nancy<br><br><br>