[gmx-users] fake atoms creation and causes a 1-4 interaction between atoms warning
Mark Abraham
mark.j.abraham at gmail.com
Thu Apr 11 22:35:08 CEST 2013
Like I said yesterday when you posted this question from a different email
account...
"Your system is blowing up because it's unstable. Where did you get this
protocol? I suggest starting by reproducing something similar that has been
published :-)"
On Thu, Apr 11, 2013 at 3:11 PM, aviv naftaly <aviv.gromacs at gmail.com>wrote:
> 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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