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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