[gmx-users] cann't calculate a silver particle
Alexej Mazheika
alex.mazheika at gmail.com
Fri Jan 11 12:33:50 CET 2013
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.
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.
Alex
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>
>>> >
>>>
>>> ==============================****==========
>>>
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>> posting!
>>>
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>> >
>>>
>>>
> --
> ==============================**==========
>
> 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>
>
> ==============================**==========
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
More information about the gromacs.org_gmx-users
mailing list