Thank you for answers
I think the problem was resolved after increasing the size of the cell in 2
borh, so I understand the possible cause of the problem: somehow the molecules
were interacting with its own image (that makes sense?),when I used a non-free
program (HyperChem :::: he performed a pre-optimization with periodic boundary
conditions) this problem has not happened. Now, the question is to maintain a
more realistic density. However, I'm relieved
Best regards
Muito obrigado a todos.
Alex W. F.? Borges
Theoretical chemistry student
Goi?nia - Brazil
Em Quinta-feira, 28 de Novembro de 2013 14:16, Paolo Giannozzi <paolo.giannozzi
at uniud.it> escreveu:
Just in case: try with other pseudopotentials. I haven't
>heard any complaints about HGH pseudopotentials, but I
>cannot rule out problems in the conversion to UPF format.
>have you tried simple systems first?
>
>Paolo
>
>
>On Thu, 2013-11-28 at 05:43 -0800, Alex wrote:
>> Dear user QE.
>>
>>
>> I'm using cp.x to perform molecular dynamics of one of bulk water
>> molecules with asparagine.
>> Following protocol, I minimized the function of wave electronics with
>> stationary nuclei.
>>
>>
>> However, in the second stage, during the optimization of the geometry
>> (with damp for electrons and ions)
>> the water molecules take a non-real geometry, in which one side of the
>> molecule, the OH distance becomes 1.98 angstrorn (A).
>> The opposite side, has the normal size of the bond which is 0.97 A. I
>> confess that since I started using it very often,
>> and sometimes does not, but do not know why that. Sometimes change is
>> functional and that resolved, sometimes not.
>>
>>
>>
>>
>>
>>
>> Incoherent bond distances of water after geometry optmization? >>>>>
>> H------------------O -----------H
>> (sorry by bad graphic)
>>? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | 1.98 A|? ? ? |0.97 A|
>>
>>
>>
>>
>> Can someone help me?
>> Put my input to be analyzed.
>>
>>
>>
>>
>> &CONTROL
>>? title = 'Asp0s'
>>? calculation = 'cp',
>>? restart_mode = 'restart',
>>? ndr = 51? ? ? !already minimized wf with sd for electrons and
>> ions=none.
>>? ndw = 52,
>>? nstep? = 50000,
>>? iprint = 1,
>>? isave? = 10,
>>? tstress = .TRUE.,
>>? tprnfor = .TRUE.,
>>? dt? ? = 5.0d0,
>>? etot_conv_thr = 1.d-8,
>>? ekin_conv_thr = 1.d-4,
>>? forc_conv_thr = 1.d-4,
>>? prefix = 'asp'
>>? pseudo_dir = 'pseudo/'
>>? outdir = './'
>> /
>>
>>
>> &SYSTEM
>>? ibrav = 1,
>>? celldm(1) = 20,
>>? celldm(2) = 0.0,
>>? celldm(3) = 0.0,
>>? celldm(4) = 0.0,
>>? celldm(5) = 0.0,
>>? celldm(6) = 0.0,
>>? nat? = 122,
>>? ntyp = 4,
>>? ecutwfc = 70.0,
>> /
>>
>>
>> &ELECTRONS
>>? emass = 400.d0,
>>? emass_cutoff = 2.5d0,
>>? orthogonalization = 'ortho',
>>? electron_dynamics = 'damp',
>>? electron_damping = 0.1
>>? ortho_max = 500,
>>? !electron_temperature = 'not_controlled',
>>? !electron_velocities = 'zero'
>> /
>>
>>
>> &IONS
>>? ion_dynamics = 'damp',
>>? ion_damping = 0.01,
>>? !ion_nstepe = 10,
>>? !ion_temperature = 'nose',
>>? !tempw = 350,
>>? !fnosep = 70,
>>? !ion_velocities = 'zero'
>> /
>>
>>
>>
>>
>> ATOMIC_SPECIES
>>
>>
>>? O 16.0d0? O.pbe-hgh.UPF
>>? H 1.0d0? H.pbe-hgh.UPF
>>? C 12.0d0? C.pbe-hgh.UPF
>>? N 14.0d0? N.pbe-hgh.UPF
>>
>>
>> ATOMIC_POSITIONS {angstrom}
>>
>>
>>? ? C? ? -0.244144? ? 1.783022? ? -1.335832
>>? ? C? ? -2.567204? ? -0.241389? ? 5.783803
>>? ? N? ? -1.038197? ? -1.652589? ? 5.418683
>>? ? C? ? -6.336078? ? -1.532299? ? -1.532562
>>? ? O? ? -5.122808? ? -0.424258? ? -2.279843
>>? ? N? ? ? 3.987336? ? 0.412822? ? -1.692063
>>? ? C? ? ? 0.552282? ? -0.043486? ? 0.368085
>>? ? O? ? ? 1.73575? ? ? 0.043368? ? 0.476670
>>? ? O? ? ? 1.126133? ? -1.181319? ? 1.757325
>>? ? H? ? -0.844512? ? -1.781630? ? -0.580034
>>? ? H? ? -1.992345? ? -1.968023? ? 0.581635
>>? ? H? ? -1.547999? ? -0.018973? ? 1.618910
>>? ? H? ? -1.017864? ? 1.793541? ? 0.067225
>>? ? H? ? -2.180408? ? 0.669590? ? -0.675764
>>? ? H? ? ? 1.490782? ? 1.185685? ? -2.387313
>>? ? H? ? ? 1.070763? ? 1.992771? ? -0.909308
>>? ? H? ? ? 0.490233? ? -1.888235? ? 1.458829
>>? ? O? ? ? 5.160929? ? 1.400891? ? -4.018523
>>? ? H? ? ? 5.585303? ? 1.845186? ? -4.767840
>>? ? H? ? ? 5.903707? ? 1.074826? ? -3.488501
>>? ? O? ? ? 6.523016? ? -2.630620? ? -1.333026
>>? ? H? ? ? 6.731773? ? -1.730291? ? -1.624223
>>? ? H? ? ? 6.238875? ? -2.519196? ? -0.413345
>> ( ........)
>>
>>
>>
>>
>> Alex.
>> Thanks to all.
>> _______________________________________________
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>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>--
>Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
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