Hello,<br><br>I am trying to simulate a simple system of ethylene glycol (ethane-1,2-diol) solvated in a water box. I converted the pdb file to a mol2 file and used topolbuild 1.2.1 to generate topology files:<br><br>$ topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6<br>
<br>I the used editconf to enlarge the box. I then solvated the molecule using the following command:<br><br>$ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -box 3 3 3 -p ethanediol.top<br><br>where "ethanediol_box.gro" is the structure of the molecule. I used grompp to generate the mdrun input file:<br>
<br>$ grompp -f grompp.mdp -c ethanediol_solv.gro -p ethanediol.top -o ethanediol.tpr<br><br>grompp.mdp is the following:<br><br>========================================<br>title = Ethanediol<br>cpp = /lib/cpp<br>
include = -I../top<br>define = <br>integrator = md<br>dt = 0.002<br>nsteps = 50000<br>nstxout = 1<br>nstvout = 5<br>
nstlog = 5<br>nstenergy = 10<br>nstxtcout = 1<br>xtc_grps = EDO SOL<br>energygrps = EDO SOL<br>nstlist = 10<br>ns_type = grid<br>
rlist = 0.8<br>coulombtype = cut-off<br>rcoulomb = 1.4<br>rvdw = 0.8<br>tcoupl = Berendsen<br>tc-grps = EDO SOL<br>tau_t = 0.1 0.1<br>
ref_t = 300 300<br>Pcoupl = Berendsen<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>gen_vel = yes<br>gen_temp = 300<br>
gen_seed = 173529<br>constraints = all-bonds<br>========================================<br><br>where "EDO" refers to ethylene glycol. grompp creates several notes:<br><br>NOTE 1 [file grompp.mdp, line unknown]:<br>
The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.<br><br>NOTE 2 [file grompp.mdp, line unknown]:<br> You are using a plain Coulomb cut-off, which might produce artifacts.<br>
You might want to consider using PME electrostatics.<br><br>NOTE 3 [file grompp.mdp, line unknown]:<br> This run will generate roughly 2500 Mb of data<br><br>I then run the simulation:<br><br>$ mdrun -s ethanediol.tpr -o traj.trr -x traj.xtc -v<br>
<br>However mdrun produces several errors and warnings:<br><br>t = 0.036 ps: Water molecule starting at atom 2659 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>t = 0.038 ps: Water molecule starting at atom 2659 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>t = 0.040 ps: Water molecule starting at atom 2659 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>Step 21 Warning: pressure scaling more than 1%, mu: 1.0372 1.0372 1.0372<br><br>Step 29, time 0.058 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>rms 2.714709, max 3.541824 (between atoms 2 and 3)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 1 4 88.8 0.6606 0.6855 0.1520<br>
2 3 90.6 0.4305 0.4542 0.1000<br> 1 2 89.2 0.6123 0.4690 0.1435<br> 5 6 93.4 0.4193 0.1741 0.1000<br> 4 5 89.2 0.6156 0.5033 0.1435<br>
===================================<br><br><br>I am not sure where the errors are occuring (I am also wondering if the absence of explicit non-polar hydrogens in the .gro files are relevant). Please adivse.<br><br>Thanks.<br>
<br>Nancy<br><br><br><br><br>