[gmx-users] fake atoms creation and causes a 1-4 interaction between atoms warning
aviv naftaly
aviv.gromacs at gmail.com
Thu Apr 11 15:11:25 CEST 2013
hi
i am using gromacs 4.5 and i am trying to run an energy minimization and
then temperature equilibration for a system of two charged plates plates
solvented in water.
the plates are made of fake atoms which has carbon atoms parameters, and a
bond length of 0.2 nm.
the plates are made from o configuration of 6x6 of these atoms. each
located in a distance of 0.2 nm from the other.
energy minimization is working just fine, but as i try to run the
temperature equilibration i get the following warning:
Warning: 1-4 interaction between 49 and 67 at distance 6.967 which is
larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
and also a bunch of these warnings:
t = 0.019 ps: Water molecule starting at atom 8260 can not be settled.
the EM file is:
title = Test_mg_water
cpp = /usr/bin/cpp -traditional; the c pre-processor
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 100000
nstxout = 100
nstlist = 1
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
fourierspacing = 0.12
optimize_fft = yes
pme_order = 4
ewald_rtol = 1e-5
;
; Energy minimizing stuff
;
emtol = 100.0
emstep = 0.01
; freeze the solute and ions
freezegrps = GAP GAN
freezedim = Y Y Y Y Y Y
energygrps = GAP GAN
*************************** (GAP and GAN are the charged plates)
the temperature equilibration file is:
title = Heat at constant volume
cpp = /usr/bin/cpp -traditional; the c pre-processor
;
define = -DPOSRES
;
constraints = none
nstlist = 1
pbc = xyz
rlist = 1.0
;domain-decomposition = yes
coulombtype = PME-switch
rcoulomb = 0.9
epsilon-r = 1
vdw-type = switch
rvdw-switch = 0.8
rvdw = 0.9
DispCorr = EnerPres
epsilon_surface = 0
integrator = sd
tinit = 0
dt = 0.002
nsteps = 37500 ; 75 psec
nstcomm = 1000
nstfout = 0
;kys
nstlog = 1000
nstenergy = 100
nstxtcout = 100
nstxout = 100
nstvout = 50000
xtc_precision = 1000
xtc_grps = SYSTEM
ns_type = grid
tc_grps = SYSTEM
tau_t = 0.1
ref_t = 300
;tcoupl = nose-hoover
;constraints = hbonds
constraint-algorithm = Lincs
;unconstrained-start = no
shake-tol = 0.0001
lincs-order = 4
lincs-warnangle = 30
lincs_iter = 2
;freezegrps = SFP SFN
;freezedim = Y Y Y Y Y Y
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Type of annealing for each temperature group (no/single/periodic)
annealing = single
; Number of time points to use for specifying annealing in each group
annealing_npoints = 4
; List of times at the annealing points for each group
annealing_time = 0 25 50 75
; Temp. at each annealing point, for each group.
annealing_temp = 5 150 300 300
gen_seed = 6594
gen_temp = 5
the initial coordinates of the plates are:
Good ROcking Metal Altar for Chronical Sinners
72
1GAP G1 1 1.750 2.000 1.750
1GAP G2 2 1.750 2.000 1.950
1GAP G3 3 1.750 2.000 2.150
1GAP G4 4 1.750 2.000 2.350
1GAP G5 5 1.750 2.000 2.550
1GAP G6 6 1.750 2.000 2.750
1GAP G7 7 1.950 2.000 1.750
1GAP G8 8 1.950 2.000 1.950
1GAP G9 9 1.950 2.000 2.150
1GAP G10 10 1.950 2.000 2.350
1GAP G11 11 1.950 2.000 2.550
1GAP G12 12 1.950 2.000 2.750
1GAP G13 13 2.150 2.000 1.750
1GAP G14 14 2.150 2.000 1.950
1GAP G15 15 2.150 2.000 2.150
1GAP G16 16 2.150 2.000 2.350
1GAP G17 17 2.150 2.000 2.550
1GAP G18 18 2.150 2.000 2.750
1GAP G19 19 2.350 2.000 1.750
1GAP G20 20 2.350 2.000 1.950
1GAP G21 21 2.350 2.000 2.150
1GAP G22 22 2.350 2.000 2.350
1GAP G23 23 2.350 2.000 2.550
1GAP G24 24 2.350 2.000 2.750
1GAP G25 25 2.550 2.000 1.750
1GAP G26 26 2.550 2.000 1.950
1GAP G27 27 2.550 2.000 2.150
1GAP G28 28 2.550 2.000 2.350
1GAP G29 29 2.550 2.000 2.550
1GAP G30 30 2.550 2.000 2.750
1GAP G31 31 2.750 2.000 1.750
1GAP G32 32 2.750 2.000 1.950
1GAP G33 33 2.750 2.000 2.150
1GAP G34 34 2.750 2.000 2.350
1GAP G35 35 2.750 2.000 2.550
1GAP G36 36 2.750 2.000 2.750
2GAN G1 37 1.750 5.000 1.750
2GAN G2 38 1.750 5.000 1.950
2GAN G3 39 1.750 5.000 2.150
2GAN G4 40 1.750 5.000 2.350
2GAN G5 41 1.750 5.000 2.550
2GAN G6 42 1.750 5.000 2.750
2GAN G7 43 1.950 5.000 1.750
2GAN G8 44 1.950 5.000 1.950
2GAN G9 45 1.950 5.000 2.150
2GAN G10 46 1.950 5.000 2.350
2GAN G11 47 1.950 5.000 2.550
2GAN G12 48 1.950 5.000 2.750
2GAN G13 49 2.150 5.000 1.750
2GAN G14 50 2.150 5.000 1.950
2GAN G15 51 2.150 5.000 2.150
2GAN G16 52 2.150 5.000 2.350
2GAN G17 53 2.150 5.000 2.550
2GAN G18 54 2.150 5.000 2.750
2GAN G19 55 2.350 5.000 1.750
2GAN G20 56 2.350 5.000 1.950
2GAN G21 57 2.350 5.000 2.150
2GAN G22 58 2.350 5.000 2.350
2GAN G23 59 2.350 5.000 2.550
2GAN G24 60 2.350 5.000 2.750
2GAN G25 61 2.550 5.000 1.750
2GAN G26 62 2.550 5.000 1.950
2GAN G27 63 2.550 5.000 2.150
2GAN G28 64 2.550 5.000 2.350
2GAN G29 65 2.550 5.000 2.550
2GAN G30 66 2.550 5.000 2.750
2GAN G31 67 2.750 5.000 1.750
2GAN G32 68 2.750 5.000 1.950
2GAN G33 69 2.750 5.000 2.150
2GAN G34 70 2.750 5.000 2.350
2GAN G35 71 2.750 5.000 2.550
2GAN G36 72 2.750 5.000 2.750
4.50000 7.00000 4.50000
the 4.5 7 4.5 are the dimentions of the box/
when i try to run the temperature equilibration simulation, the atoms of
the plate move and set in a new array with distance of 0.3 nm between them,
instead of the 0.2 nm distance which is defined for them.
as i am using amber99 force field, my G atoms are defined such that the
bond length is 0.2 nm.
in the ffamber99bon.itp file the G atom definition is:
; i j func b0 kb
G G 1 0.20000 259408.0
(in the ffamber99nb.itp the G is defined as:
name bond_type mass charge ptype sigma epsilon
amber99_70 G 0.0000 0.0000 A 1.00000e-01 3.59824e-01
though the problem is not due to water-surface interaction)
i wish to know why i keep gettig this warnings:
Warning: 1-4 interaction between 49 and 67 at distance 6.967 which is
larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
and also wish to know why the atoms of the plate are moving apart from each
other.
i guess it is related to definitions of these fake atoms, but i do not know
what i do wrong, and what do i need to do in order to define a new fake
atom appropriately.
thanks
aviv
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