Hello, I have successfully minimised and equilibrated ethylene glycol in a water box. I have noticed that there seem to be no hydrogen bonds between the solute and solvent, but there are hydrogen bonds forming and breaking between solvent molecules. Is this a normal behavior during minimsation and equilibration?
I am now trying to run MD on glycerol. I start with a "glycerol.mol2" file which contains the structure of glycerol. I am using the following commands to setup and run minimisation and equilibration on glycerol: $ .../topolbuild1_2_1/src/topolbuild -n glycerol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 I modified the "defaults" part of the "ffglycerol.itp" (generated by topolbuild) file to read: =========================== [ defaults ] ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 =========================== $ editconf -f glycerol.gro -o glycerol_box.gro -box 2.65 2.65 2.65 $ genbox -cp glycerol_box.gro -cs spc216.gro -o glycerol_solv.gro -p glycerol.top -box 2.65 2.65 2.65 $ grompp -f em.mdp -c glycerol_solv.gro -p glycerol.top -o em.tpr my "em.mdp" file is as follows: =========================== constraints = none integrator = steep nsteps = 10000 emtol = 10.0 emstep = 0.01 nstlist = 2 coulombtype = PME nstcomm = 2 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.3 nstxout = 2 pbc = xyz pme_order = 4 =========================== $ mdrun -v -deffnm em the last few lines of output are: =============================================================== Step= 6990, Dmax= 4.7e-04 nm, Epot= -3.34590e+04 Fmax= 9.13695e+01, atom= 4 Step= 6992, Dmax= 2.8e-04 nm, Epot= -3.34590e+04 Fmax= 1.40130e+02, atom= 5 Step= 6993, Dmax= 3.4e-04 nm, Epot= -3.34591e+04 Fmax= 8.57813e+01, atom= 4 Step= 6994, Dmax= 4.0e-04 nm, Epot= -3.34591e+04 Fmax= 2.41887e+02, atom= 5 Step= 6995, Dmax= 4.8e-04 nm, Epot= -3.34592e+04 Fmax= 9.36159e+01, atom= 4 Step= 6999, Dmax= 7.3e-05 nm, Epot= -3.34592e+04 Fmax= 4.95606e+01, atom= 4 Step= 7006, Dmax= 1.4e-06 nm, Epot= -3.34592e+04 Fmax= 4.89221e+01, atom= 4 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 7007 steps, but did not reach the requested Fmax < 10. Potential Energy = -3.3459230e+04 Maximum force = 4.9560604e+01 on atom 4 Norm of force = 3.4399371e+00 =============================================================== As I believe these forces to be acceptable, I proceed to equilibration: $ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr where my "nvt.mdp" file is: =========================== title = Glycerol NVT equilibration define = -DPOSRES integrator = md nsteps = 5000 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 = 1.3 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = GOL 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 =========================== where "GOL" refers to GlycerOL. $ mdrun -v -deffnm nvt When I execute the above command, I get numerous errors of the following type: =============================================================== Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.326337, max 0.500490 (between atoms 1 and 3) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'glycerol.pdb in water' 5000 steps, 10.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.663850, max 1.227203 (between atoms 1 and 7) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 3 172.3 0.2091 0.1644 0.2004 7 9 164.1 0.2082 0.1625 0.2004 2 3 124.5 0.1022 0.0787 0.1000 1 2 148.3 0.1477 0.0882 0.1435 5 6 30.4 0.0992 0.1265 0.1000 8 9 134.1 0.1014 0.0660 0.1000 7 8 138.2 0.1476 0.0991 0.1435 Warning: 1-4 interaction between 2 and 7 at distance 6.002 which is larger than the 1-4 table size 2.300 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 0.004 ps: Water molecule starting at atom 1234 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates There were 12 inconsistent shifts. Check your topology Segmentation fault =============================================================== I don't know what is happening wrong. Please advise. Thank you. Nancy
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