I agree that Justin is probably correct, although constraints should
technically work just fine with a highly dynamic reference group. Any
problems should show up as the system blowing up, but not in correctly
setting the position. I think that the problems can arise, however,
when you have multiple competing constraints. You might, for example,
try without constraining the octane bonds -- I think that you should
get perfect match in that case. Also, it is worth comparing in single
and double precision.
Still, I am not sure that you actually did a proper comparison for the
following 2 reasons:
1. you have apparently different masses for the pulled group:
Pull group 1: 15 atoms, mass 194.194
Pull group 1: 15 atoms, mass 146.146
2. you used very different starting depth offsets: -2.81855 is not
very close to -1.60929
PS: I would personally prefer if you avoided jumping directly to a bug
report unless you are sure of it. There is always at least the
possibility that you are not using the code correctly.
Chris.
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?
Thank you in advance
Karel
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