[gmx-users] (no subject)

Liron Cohen liron.cohen at weizmann.ac.il
Wed Apr 10 15:49:06 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/

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

thanks
aviv





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