[gmx-users] cann't calculate a silver particle

Alexej Mazheika alex.mazheika at gmail.com
Thu Jan 10 12:14:25 CET 2013


Hi all!

I am new in MD and in Gromacs. I try to calculate the structure of an Ag125
particle in the gas phase. But during the optimization, all silver atoms
fly apart around the cell. So no cluster exists at the end even by
relatively low temperatures. The constants for LJ potential I took from
experimental data. I guess that something can be wrong in the grompp.mdp,
which I took from examples in share/tutor/ and modified a bit, but I cann't
understand what's the matter. Input files are shown below

Alex

*conf.gro:*

Bulk silver, t = 0.0
  125
 0001Clust   Ag    1   0.000   0.000   0.000
 0002Clust   Ag    2   0.204   0.204   0.000
 0003Clust   Ag    3   0.409   0.409   0.000
 0004Clust   Ag    4  -0.409  -0.409   0.000
 0005Clust   Ag    5  -0.204  -0.204   0.000
 0006Clust   Ag    6   0.204   0.000   0.204
 0007Clust   Ag    7   0.409   0.204   0.204
 0008Clust   Ag    8   0.613   0.409   0.204
 0009Clust   Ag    9  -0.204  -0.409   0.204
 0010Clust   Ag   10   0.000  -0.204   0.204
 0011Clust   Ag   11   0.409   0.000   0.409
 0012Clust   Ag   12   0.613   0.204   0.409
 0013Clust   Ag   13   0.817   0.409   0.409
 0014Clust   Ag   14   0.000  -0.409   0.409
 0015Clust   Ag   15   0.204  -0.204   0.409
 0016Clust   Ag   16  -0.409   0.000  -0.409
 0017Clust   Ag   17  -0.204   0.204  -0.409
 0018Clust   Ag   18   0.000   0.409  -0.409
 0019Clust   Ag   19  -0.817  -0.409  -0.409
 0020Clust   Ag   20  -0.613  -0.204  -0.409
 0021Clust   Ag   21  -0.204   0.000  -0.204
 0022Clust   Ag   22   0.000   0.204  -0.204
 0023Clust   Ag   23   0.204   0.409  -0.204
 0024Clust   Ag   24  -0.613  -0.409  -0.204
 0025Clust   Ag   25  -0.409  -0.204  -0.204
 0026Clust   Ag   26   0.000   0.204   0.204
 0027Clust   Ag   27   0.204   0.409   0.204
 0028Clust   Ag   28   0.409   0.613   0.204
 0029Clust   Ag   29  -0.409  -0.204   0.204
 0030Clust   Ag   30  -0.204   0.000   0.204
 0031Clust   Ag   31   0.204   0.204   0.409
 0032Clust   Ag   32   0.409   0.409   0.409
 0033Clust   Ag   33   0.613   0.613   0.409
 0034Clust   Ag   34  -0.204  -0.204   0.409
 0035Clust   Ag   35   0.000   0.000   0.409
 0036Clust   Ag   36   0.409   0.204   0.613
 0037Clust   Ag   37   0.613   0.409   0.613
 0038Clust   Ag   38   0.817   0.613   0.613
 0039Clust   Ag   39   0.000  -0.204   0.613
 0040Clust   Ag   40   0.204   0.000   0.613
 0041Clust   Ag   41  -0.409   0.204  -0.204
 0042Clust   Ag   42  -0.204   0.409  -0.204
 0043Clust   Ag   43   0.000   0.613  -0.204
 0044Clust   Ag   44  -0.817  -0.204  -0.204
 0045Clust   Ag   45  -0.613   0.000  -0.204
 0046Clust   Ag   46  -0.204   0.204   0.000
 0047Clust   Ag   47   0.000   0.409   0.000
 0048Clust   Ag   48   0.204   0.613   0.000
 0049Clust   Ag   49  -0.613  -0.204   0.000
 0050Clust   Ag   50  -0.409   0.000   0.000
 0051Clust   Ag   51   0.000   0.409   0.409
 0052Clust   Ag   52   0.204   0.613   0.409
 0053Clust   Ag   53   0.409   0.817   0.409
 0054Clust   Ag   54  -0.409   0.000   0.409
 0055Clust   Ag   55  -0.204   0.204   0.409
 0056Clust   Ag   56   0.204   0.409   0.613
 0057Clust   Ag   57   0.409   0.613   0.613
 0058Clust   Ag   58   0.613   0.817   0.613
 0059Clust   Ag   59  -0.204   0.000   0.613
 0060Clust   Ag   60   0.000   0.204   0.613
 0061Clust   Ag   61   0.409   0.409   0.817
 0062Clust   Ag   62   0.613   0.613   0.817
 0063Clust   Ag   63   0.817   0.817   0.817
 0064Clust   Ag   64   0.000   0.000   0.817
 0065Clust   Ag   65   0.204   0.204   0.817
 0066Clust   Ag   66  -0.409   0.409   0.000
 0067Clust   Ag   67  -0.204   0.613   0.000
 0068Clust   Ag   68   0.000   0.817   0.000
 0069Clust   Ag   69  -0.817   0.000   0.000
 0070Clust   Ag   70  -0.613   0.204   0.000
 0071Clust   Ag   71  -0.204   0.409   0.204
 0072Clust   Ag   72   0.000   0.613   0.204
 0073Clust   Ag   73   0.204   0.817   0.204
 0074Clust   Ag   74  -0.613   0.000   0.204
 0075Clust   Ag   75  -0.409   0.204   0.204
 0076Clust   Ag   76   0.000  -0.409  -0.409
 0077Clust   Ag   77   0.204  -0.204  -0.409
 0078Clust   Ag   78   0.409   0.000  -0.409
 0079Clust   Ag   79  -0.409  -0.817  -0.409
 0080Clust   Ag   80  -0.204  -0.613  -0.409
 0081Clust   Ag   81   0.204  -0.409  -0.204
 0082Clust   Ag   82   0.409  -0.204  -0.204
 0083Clust   Ag   83   0.613   0.000  -0.204
 0084Clust   Ag   84  -0.204  -0.817  -0.204
 0085Clust   Ag   85   0.000  -0.613  -0.204
 0086Clust   Ag   86   0.409  -0.409   0.000
 0087Clust   Ag   87   0.613  -0.204   0.000
 0088Clust   Ag   88   0.817   0.000   0.000
 0089Clust   Ag   89   0.000  -0.817   0.000
 0090Clust   Ag   90   0.204  -0.613   0.000
 0091Clust   Ag   91  -0.409  -0.409  -0.817
 0092Clust   Ag   92  -0.204  -0.204  -0.817
 0093Clust   Ag   93   0.000   0.000  -0.817
 0094Clust   Ag   94  -0.817  -0.817  -0.817
 0095Clust   Ag   95  -0.613  -0.613  -0.817
 0096Clust   Ag   96  -0.204  -0.409  -0.613
 0097Clust   Ag   97   0.000  -0.204  -0.613
 0098Clust   Ag   98   0.204   0.000  -0.613
 0099Clust   Ag   99  -0.613  -0.817  -0.613
 0100Clust   Ag  100  -0.409  -0.613  -0.613
 0101Clust   Ag  101   0.000  -0.204  -0.204
 0102Clust   Ag  102   0.204   0.000  -0.204
 0103Clust   Ag  103   0.409   0.204  -0.204
 0104Clust   Ag  104  -0.409  -0.613  -0.204
 0105Clust   Ag  105  -0.204  -0.409  -0.204
 0106Clust   Ag  106   0.204  -0.204   0.000
 0107Clust   Ag  107   0.409   0.000   0.000
 0108Clust   Ag  108   0.613   0.204   0.000
 0109Clust   Ag  109  -0.204  -0.613   0.000
 0110Clust   Ag  110   0.000  -0.409   0.000
 0111Clust   Ag  111   0.409  -0.204   0.204
 0112Clust   Ag  112   0.613   0.000   0.204
 0113Clust   Ag  113   0.817   0.204   0.204
 0114Clust   Ag  114   0.000  -0.613   0.204
 0115Clust   Ag  115   0.204  -0.409   0.204
 0116Clust   Ag  116  -0.409  -0.204  -0.613
 0117Clust   Ag  117  -0.204   0.000  -0.613
 0118Clust   Ag  118   0.000   0.204  -0.613
 0119Clust   Ag  119  -0.817  -0.613  -0.613
 0120Clust   Ag  120  -0.613  -0.409  -0.613
 0121Clust   Ag  121  -0.204  -0.204  -0.409
 0122Clust   Ag  122   0.000   0.000  -0.409
 0123Clust   Ag  123   0.204   0.204  -0.409
 0124Clust   Ag  124  -0.613  -0.613  -0.409
 0125Clust   Ag  125  -0.409  -0.409  -0.409
    4.00000    4.00000    4.00000

*grompp.mdp:*

title                    = Yo
cpp                      = /usr/bin/cpp
include                  =
define                   =

integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 10000
init_step                = 0
comm-mode                = Linear
nstcomm                  = 1
comm-grps                =

bd-temp                  = 300
bd-fric                  = 0
ld-seed                  = 1993

nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstcheckpoint            = 1000
nstlog                   = 50
nstenergy                = 50
nstxtcout                = 50
xtc-precision            = 1000
xtc-grps                 =
energygrps               =

nstlist                  = 3
ns_type                  = grid
pbc                      = xyz
rlist                    = 0.9
domain-decomposition     = no

coulombtype              = Cut-off
rcoulomb-switch          = 0
rcoulomb                 = 0.9
epsilon-r                = 1
vdw-type                 = Cut-off
rvdw-switch              = 0
rvdw                     = 1.2
DispCorr                 = EnerPres
table-extension          = 1

Tcoupl                   = berendsen
tc-grps                  = System
tau_t                    = 0.1
ref_t                    = 300
Pcoupl                   = berendsen
Pcoupltype               = isotropic
tau_p                    = 0.1
compressibility          = 4.5e-5
ref_p                    = 1.0
andersen_seed            = 815131

gen_vel                  = yes
gen_temp                 = 100
gen_seed                 = 1993

constraints              = none
morse                    = no

energygrp_excl           =

*topol.top:*

#include "amber03.ff/forcefield.itp"
#include "silver.itp"

[ moleculetype ]
0001Clust    1

[ atoms ]
1       Ag       1       Ag      Ag      1        0.000

[ system ]
Bulk silver

[ molecules ]
0001Clust  125

*silver.itp:*

[ atomtypes ]
    Ag        107.8682    0.0     A    3.3156e-1      9.6468e-5



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