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

Justin Lemkul jalemkul at vt.edu
Fri Jan 11 11:32:09 CET 2013



On 1/11/13 5:02 AM, Alexej Mazheika wrote:
> Hello
>
> I removed PBC and set space conditions as you recommended. I also modified
> a bit the grompp.mdp (new version is below). However, it did not help to
> prevent the scattering of silver atoms in all directions. The change of
> parameters in LJ doesn't influence on the final geometry. It seems, that LJ
> coefficients don't play any role at all! The decrease of the temperature
> (from 300 to 100K) provides only smaller radius of the cloud of flown apart
> Ag-atoms. So no Ag125 particle exists at the end. It looks like it doesn't
> recognise the silver.itp with atom parameters, which I designated in
> topol.top.
>

If that were true, you would have gotten a fatal error when running grompp.  You 
can always validate the contents of the .tpr file using gmxdump to prove to 
yourself that all the correct information is there.  Do you have sufficient 
evidence to suggest that those parameters should indeed stabilize the cluster of 
silver atoms?  Have these parameters been validated and determined to be 
appropriate for use with the (biomolecular) AMBER03 force field?

-Justin

> *grompp.mdp*:
>
> title                    = Yo
> cpp                      = /usr/bin/cpp
>
> integrator               = md
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 10000
> init_step                = 0
> comm-mode                = ANGULAR
> nstcomm                  = 1
>
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstcheckpoint            = 1000
> nstlog                   = 50
> nstenergy                = 50
> nstxtcout                = 50
> xtc-precision            = 1000
>
> nstlist                  = 0
> ns_type                  = grid
> pbc                      = no
> rlist                    = 0
> domain-decomposition     = no
>
> coulombtype              = Cut-off
> rcoulomb-switch          = 0
> rcoulomb                 = 0
> epsilon-r                = 1
> vdw-type                 = Cut-off
> rvdw-switch              = 0
> rvdw                     = 0
>
> Tcoupl                   = v-rescale
> tc-grps                  = System
> tau_t                    = 0.1
> ref_t                    = 300
> ld-seed                  = 1993
> Pcoupl                   = no
> andersen_seed            = 815131
>
> annealing                = no
>
> gen_vel                  = yes
> gen_temp                 = 1
> gen_seed                 = 1993
> constraints              = none
> morse                    = no
>
>
> On Thu, Jan 10, 2013 at 4:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/10/13 6:14 AM, Alexej Mazheika wrote:
>>
>>> 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           =
>>>
>>>
>> You're not actually simulating in the gas phase with these parameters, and
>> I'm surprised the simulation worked at all.  With pressure coupling, the
>> unit cell should probably have collapsed, and even if it didn't, you're
>> simulating in some sort of pseudo-crystal state.  I posted about this
>> yesterday...
>>
>> In any case, what you should be doing is more along the lines of:
>>
>> pbc = no
>> rvdw = 0
>> rcoulomb = 0
>> rlist = 0
>> nstlist = 0
>> pcoupl = no
>>
>> This will give you a fixed neighbor list with infinite cutoffs in a more
>> reasonable representation of the gas phase.
>>
>> -Justin
>>
>>   *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
>>>
>>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
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>>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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