Krapnik wrote:
Dear all,
we are trying to simulate molecule in specified depth in octanol to
calculate logP.
for this purpose we have used box with slab of octanol, molecule in
specified distance in z-axis and this mdp:
integrator = md
dt = 0.002
tinit = 0
nsteps = 5125000 ; 10.250 ns
nstcomm = 1
comm_mode = Linear
; Output parameters
nstxout = 0 ; every 1 ns
nstvout = 0
nstfout = 0
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraints = all-bonds
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc_grps = System
tau_t = 0.1
ref_t = 310
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = anisotropic ; anisotropic pressure coupling
tau_p = 10
compressibility = 0 0 4.5e-5 0 0 0 ; since octanol tries to separate
from water and shortening xy plane
ref_p = 1.0 1.0 1.0 0 0 0
; Pull code
pull = constraint ;
pull_geometry = distance ; Pull along the vector connecting the
two groups. Components can be selected with pull_dim.
pull_dim = N N Y ; put potential only to axis z
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1 ; one group to pull
pull_group0 = OCT ; reference group (can be empty to set
it to 0,0,0)
pull_group1 = DRG
pull_rate1 = 0 ; 0.01 nm per ps = 10 nm per ns = 10 m per s
pull_k1 = 2000 ; kJ mol^-1 nm^-2
however when I list pull-x.xvg I obtain:
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.0000 6.06871 -2.81855
0.0200 6.07793 -2.81861
0.0400 6.08787 -2.81856
0.0600 6.08462 -2.81855
0.0800 6.10028 -2.82007
The situation is even more strange when almost the same mdp with DOPC
membrane works fine as can be seen in pull-x.xvg:
0.0000 3.72735 -1.60929
0.0200 3.72727 -1.60929
0.0400 3.7272 -1.60929
0.0600 3.72716 -1.60929
0.0800 3.72715 -1.60929
0.1000 3.72717 -1.60929
Differences in the working case in mdp are only this:
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p = 1.0 1.0 1.0 0 0 0
pull_group0 = DOPC
Strangerly enough - the same happens in GMX4.0.7 and in GMX4.5.3
I wonder where the difference is, as both logs states that
Will apply constraint COM pulling in geometry 'distance'
between a reference group and 1 group
Pull group 0: 6912 atoms, mass 100624.859
Pull group 1: 15 atoms, mass 194.194
Will apply constraint COM pulling in geometry 'distance'
between a reference group and 1 group
Pull group 0: 9570 atoms, mass 124631.453
Pull group 1: 15 atoms, mass 146.146
Where should I look and repair?
I don't see any real problem here. The DOPC membrane probably holds its shape
better than the octanol slab and thus the reference position (which determines
the constraint) is less mobile. As such, the constraint is more stable in DOPC
than in octanol. The slight bump in the octanol system amounts to a change of
0.16%, which I'd say is quite small. You're also looking at the first few
frames of the simulation, which may amount to equilibration, but you haven't
mentioned if you've done anything prior to this run.
As long as there is no systematic change in position, I'd say there's no
problem.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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