[gmx-users] MD Simulation Errors for Ethylene Glycol-Water System

[Nancy]

Hello,

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:

$ topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6

I the used editconf to enlarge the box.  I then solvated the molecule using
the following command:

$ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -box 3
3 3 -p ethanediol.top

where "ethanediol_box.gro" is the structure of the molecule.  I used grompp
to generate the mdrun input file:

$ grompp -f grompp.mdp -c ethanediol_solv.gro -p ethanediol.top -o
ethanediol.tpr

grompp.mdp is the following:

========================================
title                    = Ethanediol
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md
dt                       = 0.002
nsteps                   = 50000
nstxout                  = 1
nstvout                  = 5
nstlog                   = 5
nstenergy                = 10
nstxtcout                = 1
xtc_grps                 = EDO  SOL
energygrps               = EDO  SOL
nstlist                  = 10
ns_type                  = grid
rlist                    = 0.8
coulombtype              = cut-off
rcoulomb                 = 1.4
rvdw                     = 0.8
tcoupl                   = Berendsen
tc-grps                  = EDO  SOL
tau_t                    = 0.1  0.1
ref_t                    = 300  300
Pcoupl                   = Berendsen
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
constraints              = all-bonds
========================================

where "EDO" refers to ethylene glycol.  grompp creates several notes:

NOTE 1 [file grompp.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

NOTE 2 [file grompp.mdp, line unknown]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.

NOTE 3 [file grompp.mdp, line unknown]:
  This run will generate roughly 2500 Mb of data

I then run the simulation:

$ mdrun -s ethanediol.tpr -o traj.trr -x traj.xtc -v

However mdrun produces several errors and warnings:

t = 0.036 ps: Water molecule starting at atom 2659 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

t = 0.038 ps: Water molecule starting at atom 2659 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

t = 0.040 ps: Water molecule starting at atom 2659 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

Step 21  Warning: pressure scaling more than 1%, mu: 1.0372 1.0372 1.0372

Step 29, time 0.058 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.714709, max 3.541824 (between atoms 2 and 3)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      1      4   88.8    0.6606   0.6855      0.1520
      2      3   90.6    0.4305   0.4542      0.1000
      1      2   89.2    0.6123   0.4690      0.1435
      5      6   93.4    0.4193   0.1741      0.1000
      4      5   89.2    0.6156   0.5033      0.1435
===================================


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.

Thanks.

Nancy
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