[gmx-users] cann't calculate a silver particle
Justin Lemkul
jalemkul at vt.edu
Fri Jan 11 13:02:38 CET 2013
On 1/11/13 6:33 AM, Alexej Mazheika wrote:
> Dear Justin,
>
> The grompp doesn't show any fatal error. Using gmxdump I have checked the
> topol.tpr file, and I found that C6 and C12 parameters of LJ have there
> completely different values in contrast to those I wrote in silver.itp!
> Maybe it is the reason. But I wrote parameters in *.itp in units of
> [E]=kJ/mol and [r]=nm. The C6 and C12 constants were taken from
> experimental data of bulk silver (from lattice constant and enthalpy of
> formation), so they must be right.
AMBER force fields do not specify nonbonded parameters in terms of C6 and C12,
they are written as sigma and epsilon. If you're using C6 and C12 directly,
then the parameters are in fact wrong within the context of what the force field
expects. See the manual for the conversion equations or use g_sigeps.
> Concerning AMBER03 force field, I am new in MD and I do not know exactly
> how to check the validation of LJ parameters applying it.
>
I wasn't sure what your source was for the parameters. I would still encourage
you to consult AMBER literature for how parameters are generally developed,
which typically includes QM calculations. Dealing with transition metals is a
tricky proposition for any of the force fields used in Gromacs. There's
definitely literature out there from people who have simulated metal particles,
so I would suggest you also investigate what those authors do and what
parameters they use.
-Justin
> On Fri, Jan 11, 2013 at 12:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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://vt.edu/Pages/Personal/justin>
>>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>
>>>>
>>>> ==============================****==========
>>>>
>>>> --
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>>>>>
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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<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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