Nancy wrote:
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.
Take this advice. PME is substantially more accurate than plain cutoffs. Also,
re-consider your values of the cutoffs (rcoulomb, rvdw). At the very least,
rvdw is too short, given the specifics of the force field derivation.
NOTE 3 [file grompp.mdp, line unknown]:
This run will generate roughly 2500 Mb of data
Ouch. Consider setting nstxout to some value considerably greater than 1,
unless you need an exceptional amount of data. Since you have also set
nstxtcout to 1, you almost certainly don't need your .trr file to be that huge :)
Unrelated to your problem, but just FYI.
I then run the simulation:
$ mdrun -s ethanediol.tpr -o traj.trr -x traj.xtc -v
However mdrun produces several errors and warnings:
See the following:
http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
http://oldwiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25
http://oldwiki.gromacs.org/index.php/blowing_up
<snip>
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.
Not likely. It is a fundamental fact of UA force fields (like G53a6, as you
have chosen) that non-polar hydrogens are not explicitly represented. These
force fields work just fine.
What have you done in terms of energy minimization and equilibration on this
system?
-Justin
Thanks.
Nancy
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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