Hi everyone!
I'm new to Gromacs and trying to
simulate a membrane system with two walls, one at the bottom of my
box at z=0 and one at the top, using the gromos53a6 forcefield
(GROMACS version 4.5.5).
My testing system consists of a
membrane in the middle, water and sodium ions (40) above the membrane
and water and chloride ions (also 40) beneath it.
First, I built up the system, did an
energy minimization and then implemented the walls for the
nvt-equilibration. I didn't change anything in the topology. (Do I
have to define the wall-atem-type there? If yes, what exactly do I
have to put in the topology?)
My nvt.mdp file looks like that:
title = NVT equilibration
for KALP15-DPPC
define = -DSTRONG_POSRES
-DPOSRES_LIPID ; position restrain the lipid
; Run parameters
integrator = md
;
leap-frog integrator
nsteps = 50000
; 2 *
50000 = 100 ps
dt = 0.002
; 2 fs
; Output control
nstxout = 100
; save
coordinates every 0.2 ps
nstvout = 100
; save
velocities every 0.2 ps
nstenergy = 100 ;
save
energies every 0.2 ps
nstlog = 100
; update
log file every 0.2 ps
; Bond parameters
continuation = yes ;
first dynamics run
constraint_algorithm =
lincs ; holonomic constraints
constraints = all-bonds ;
all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1
; accuracy
of LINCS
lincs_order = 4 ;
also
related to accuracy
; Neighborsearching
ns_type = grid
; search
neighboring grid cels
nstlist = 5
; 10 fs
rlist = 1.2
;
short-range neighborlist cutoff (in nm)
rcoulomb = 1.2
;
short-range electrostatic cutoff (in nm)
rvdw = 1.2
; short-range
van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME
;
Particle Mesh Ewald for long-range electrostatics
pme_order = 4
; cubic
interpolation
fourierspacing = 0.16
;
grid spacing for FFT
; Temperature coupling is
on
tcoupl = V-rescale
;
modified Berendsen thermostat
tc-grps = lipid
SOL_NA_CL ; two coupling groups - more
accurate
tau_t = 0.1 0.1
;
time constant, in ps
ref_t = 303 303
;
reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no
; no
pressure coupling in NVT
; Periodic boundary
conditions
;wall
nwall = 2
wall_type = 10-4
wall_density = 100
100
wall_atomtype = C C
wall_r_linpot = 1 1 ;
with -1 I got a fatal error, because atoms were beyond the wall
wall_ewald_zfac = 3
ewald_geometry= 3dc
pbc = xy
; Periodic
Boundary Conditions in x/y direction
; Dispersion correction
DispCorr = EnerPres ;
account for cut-off vdW scheme
; Velocity generation
gen_vel = yes
; assign
velocities from Maxwell distribution
gen_temp = 303
;
temperature for Maxwell distribution
gen_seed = -1
; generate
a random seed
; COM motion removal
; These options remove
motion of the protein/bilayer relative to the solvent/ions
nstcomm = 10
comm-mode = Linear
comm-grps = lipid
SOL_NA_CL
What I see in VMD is the
following: as expected some NA-ions are going through the membrane to
reach the chloride/water side. But at the same time water molecules
(and one chloride-ion) at both sides disappear in z-direction and
never come back. In the first 10 ps (with a tiny time-step of 0.1 fs)
there were only a few molecules that went outside the box, but after
10 ps it increased dramatically and at some point the equilibration
crashed.
I already played around
with time-steps, atom_types and density, but couldn't find anything
that works to keep the molecules inside the box..
Anyone has an idea what I
did wrong and how I can correct it? Already read the manual and
mailing-list archive, but could not find anything that really helped
me....
Thank you so much in
advance!!!!
Cheers,
Marianne
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