Hello,<br><br>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?<br>
<br>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:<br>
<br>$ .../topolbuild1_2_1/src/topolbuild -n glycerol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6<br><br>I modified the "defaults" part of the "ffglycerol.itp" (generated by topolbuild) file to read:<br>
<br>===========================<br>[ defaults ]<br>;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br> 1 1 no 1.0 1.0<br>===========================<br><br>$ editconf -f glycerol.gro -o glycerol_box.gro -box 2.65 2.65 2.65<br>
$ genbox -cp glycerol_box.gro -cs spc216.gro -o glycerol_solv.gro -p glycerol.top -box 2.65 2.65 2.65<br>$ grompp -f em.mdp -c glycerol_solv.gro -p glycerol.top -o em.tpr<br><br>my "em.mdp" file is as follows:<br>
<br>===========================<br>constraints = none<br>integrator = steep<br>nsteps = 10000<br><br>emtol = 10.0<br>emstep = 0.01<br> <br>nstlist = 2<br>
coulombtype = PME<br>nstcomm = 2<br><br>ns_type = grid<br>rlist = 1.0<br>rcoulomb = 1.0<br>rvdw = 1.3<br>nstxout = 2<br><br>pbc = xyz<br>
pme_order = 4<br>===========================<br><br>$ mdrun -v -deffnm em<br><br>the last few lines of output are:<br><br>===============================================================<br>Step= 6990, Dmax= 4.7e-04 nm, Epot= -3.34590e+04 Fmax= 9.13695e+01, atom= 4<br>
Step= 6992, Dmax= 2.8e-04 nm, Epot= -3.34590e+04 Fmax= 1.40130e+02, atom= 5<br>Step= 6993, Dmax= 3.4e-04 nm, Epot= -3.34591e+04 Fmax= 8.57813e+01, atom= 4<br>Step= 6994, Dmax= 4.0e-04 nm, Epot= -3.34591e+04 Fmax= 2.41887e+02, atom= 5<br>
Step= 6995, Dmax= 4.8e-04 nm, Epot= -3.34592e+04 Fmax= 9.36159e+01, atom= 4<br>Step= 6999, Dmax= 7.3e-05 nm, Epot= -3.34592e+04 Fmax= 4.95606e+01, atom= 4<br>Step= 7006, Dmax= 1.4e-06 nm, Epot= -3.34592e+04 Fmax= 4.89221e+01, atom= 4<br>
Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 10<br><br>Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>
off constraints alltogether (set constraints = none in mdp file)<br><br>writing lowest energy coordinates.<br><br>Steepest Descents converged to machine precision in 7007 steps,<br>but did not reach the requested Fmax < 10.<br>
Potential Energy = -3.3459230e+04<br>Maximum force = 4.9560604e+01 on atom 4<br>Norm of force = 3.4399371e+00<br>===============================================================<br><br>As I believe these forces to be acceptable, I proceed to equilibration:<br>
<br>$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr<br><br>where my "nvt.mdp" file is:<br><br>===========================<br>title = Glycerol NVT equilibration <br>define = -DPOSRES<br><br>
integrator = md<br>nsteps = 5000<br>dt = 0.002<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 = GOL 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>where "GOL" refers to GlycerOL.<br><br>$ mdrun -v -deffnm nvt<br><br>When I execute the above command, I get numerous errors of the following type:<br>
<br>===============================================================<br>Step 0, time 0 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.326337, max 0.500490 (between atoms 1 and 3)<br>bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>starting mdrun 'glycerol.pdb in water'<br>5000 steps, 10.0 ps.<br><br>Step 0, time 0 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.663850, max 1.227203 (between atoms 1 and 7)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 1 3 172.3 0.2091 0.1644 0.2004<br> 7 9 164.1 0.2082 0.1625 0.2004<br>
2 3 124.5 0.1022 0.0787 0.1000<br> 1 2 148.3 0.1477 0.0882 0.1435<br> 5 6 30.4 0.0992 0.1265 0.1000<br> 8 9 134.1 0.1014 0.0660 0.1000<br>
7 8 138.2 0.1476 0.0991 0.1435<br><br>Warning: 1-4 interaction between 2 and 7 at distance 6.002 which is larger than the 1-4 table size 2.300 nm<br>These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br><br>t = 0.004 ps: Water molecule starting at atom 1234 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br><br>There were 12 inconsistent shifts. Check your topology<br>Segmentation fault<br>===============================================================<br>
<br>I don't know what is happening wrong. Please advise.<br><br>Thank you.<br><br>Nancy<br><br><br><br>