[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

Krapnik krapnik at gmail.com
Wed Aug 10 17:42:02 CEST 2011


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


Zdraví skoro zdravý
Karel "Krápník" Berka

****************************************************************
RNDr. Karel Berka, Ph.D.
Palacký University in Olomouc
Faculty of Science
Department of Physical Chemistry
tř. 17. listopadu 1192/12
771 46 Olomouc
tel: +420-585634769
fax: +420-585634769
e-mail: karel.berka at upol.cz

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