[gmx-users] (no subject)

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 10 23:06:36 CEST 2013


On Wed, Apr 10, 2013 at 3:49 PM, Liron Cohen <liron.cohen at weizmann.ac.il>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/
>
> i want to know what do i do wrong and why do i keep getting this 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
>

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 :-)

Mark



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