Hello, I am trying to equilibrate and run MD on a system of solvated ethylene glycol (ethanediol). However I am running into numerous problems.
First, I try to minimise the system. I start with an ethanediol.mol2 file which contains the structure of the molecule. $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 the above outputs the following files: ethanediol.gro ethanediol.log ethanediolMOL.mol2 ethanediol.top ffethanediol.itp posreethanediol.itp Note: the ethanediol.log file contains a section that has several lines with asterisks: ============================ Angles Force Field Results Angle Atoms force angle method measured 1 H12- C1- H11 ****** ****** ****** 109.403 2 C2- C1- H11 ****** ****** ****** 109.456 3 O1- C1- H11 ****** ****** ****** 109.438 4 C2- C1- H12 ****** ****** ****** 109.537 5 O1- C1- H12 ****** ****** ****** 109.468 6 O1- C1- C2 320.0 109.50 1 109.526 7 C1- C2- O2 320.0 109.50 1 109.526 8 C1- C2- H22 ****** ****** ****** 109.453 9 C1- C2- H21 ****** ****** ****** 109.537 10 H22- C2- O2 ****** ****** ****** 109.439 11 H21- C2- O2 ****** ****** ****** 109.468 12 C2- O2- HO2 450.0 109.50 1 106.864 13 H21- C2- H22 ****** ****** ****** 109.404 14 C1- O1- HO1 450.0 109.50 1 106.864 ============================ $ editconf -f ethanediol.gro -o ethanediol_box.gro -c -d 1.0 -bt cubic $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p ethanediol.top $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr the "minim.mdp" file is: ============================ define = -DFLEXIBLE integrator = steep emtol = 10.0 emstep = 0.01 nsteps = 2000 nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb_switch = 1.0 rvdw_switch = 1.3 pbc = xyz pme_order = 4 constraints = none nstxout = 1 nstvout = 1 nstenergy = 1 nstlog = 1 nstcomm = 1 Tcoupl = no Pcoupl = no gen_vel = no ============================ $ mdrun -v -deffnm em the last few lines of the output of the minimisation are: ============================ Step= 1990, Dmax= 1.1e-05 nm, Epot= -3.38051e+04 Fmax= 4.80304e+04, atom= 559 Step= 1991, Dmax= 1.3e-05 nm, Epot= -3.38053e+04 Fmax= 7.73723e+04, atom= 795 Step= 1992, Dmax= 1.6e-05 nm, Epot= -3.38059e+04 Fmax= 7.31046e+04, atom= 559 Step= 1994, Dmax= 9.5e-06 nm, Epot= -3.38069e+04 Fmax= 2.67253e+04, atom= 739 Step= 1995, Dmax= 1.1e-05 nm, Epot= -3.38076e+04 Fmax= 4.96799e+04, atom= 559 Step= 1996, Dmax= 1.4e-05 nm, Epot= -3.38078e+04 Fmax= 8.04458e+04, atom= 795 Step= 1997, Dmax= 1.6e-05 nm, Epot= -3.38084e+04 Fmax= 7.56146e+04, atom= 559 Step= 1999, Dmax= 9.9e-06 nm, Epot= -3.38094e+04 Fmax= 2.68226e+04, atom= 739 Step= 2000, Dmax= 1.2e-05 nm, Epot= -3.38102e+04 Fmax= 5.49575e+04, atom= 559 writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 2001 steps. Potential Energy = -3.3810168e+04 Maximum force = 5.4957539e+04 on atom 559 Norm of force = 2.7119446e+03 ============================ I have already tried increasing the number of steps, but I found no way of lowering the forces. I have found that by limiting the number of solvent molecules to ~5, I can manage to acheive lower energies, however, the amount of time it takes for a larger number of water molecules increases exponentially. So, I am trying to proceed to equilibration: $ grompp -f nvt.mdp -c em.gro -p ethanediol.top -o nvt.tpr "nvt.mdp" is: ============================ title = Ethanediol NVT equilibration define = -DFLEXIBLE integrator = md nsteps = 2000 dt = 0.002 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 = 1.2 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 ============================ Unfortunately, I receive numerous errors such as this one: ============================ Step 3, time 0.006 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.067249, max 2.300835 (between atoms 691 and 692) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 406 407 33.5 0.1005 0.0956 0.1000 692 693 91.2 0.1631 0.3470 0.1633 691 692 88.9 0.0999 0.3301 0.1000 691 693 86.0 0.0999 0.0881 0.1000 794 795 35.4 0.1707 0.1587 0.1633 793 795 59.5 0.1063 0.0995 0.1000 Wrote pdb files with previous and current coordinates Segmentation fault ============================ I believe that equilibration is failing because of the large forces on the molecules during minimisation (although I am not sure, as I was able to run a simulation without proper minimisation before). If at all possible, please advise on how to reduce the energies and forces during minimisation. Thank you. Nancy
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