Glycine optimization

Top Page > Browsing

Glycine optimization

Date: 2025/01/26 04:48
Name: dena <daa58768199@gmail.com>: Hello everyone
I prepared the structure file of the amino acid glycine in zwitterionic format as follows for optimization and ran it for optimization.
.....
pecies.Number 4
<Definition.of.Atomic.Species
H H6.0-s2p1 H_PBE19
C C6.0-s2p2d1 C_PBE19
N N6.0-s2p2d1 N_PBE19
O O6.0-s2p2d1 O_PBE19
Definition.of.Atomic.Species>

Atoms.Number 10
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 N -14.0680000 -36.8279990 22.5709990 2.5 2.5
2 H -14.4370000 -35.9230000 22.7810000 0.5 0.5
3 H -13.7530000 -36.8559990 21.6220000 0.5 0.5
4 H -13.3100000 -37.0379980 23.1880000 0.5 0.5
5 C -15.1150000 -37.8200000 22.7520010 2.0 2.0
6 H -15.9020000 -37.5719990 22.0529990 0.5 0.5
7 H -15.4140000 -37.7770000 23.7910000 0.5 0.5
8 C -14.6530000 -39.2330020 22.4570010 2.0 2.0
9 O -13.6900000 -39.2109990 22.1870000 3.0 3.0
10 O -15.4170000 -39.8620000 22.6000000 3.0 3.0
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
18.0000000 0.0000000 0.0000000
0.0000000 18.0000000 0.0000000
0.0000000 0.0000000 18.0000000
Atoms.UnitVectors>
cf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 250 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver cluster # DC|GDC|Cluster|Band
scf.Kgrid 1 1 1 # means 4x4x4
scf.Mixing.Type rmm-diis # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.10 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.40
scf.Mixing.History 10 # default=5
scf.Mixing.StartPulay 5 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)

#
# MD or Geometry Optimization
#

MD.Type RF # Nomd|Opt|NVE|NVT_VS|NVT_NH
# Constraint_Opt|DIIS2|Constraint_DIIS2
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 20 # default=5
MD.Opt.EveryDIIS 10000 # default=10
MD.maxIter 200 # default=1
MD.TimeStep 1.0 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)

After the optimization of the XYZ file was completed, the structure was checked and converted to non-zwitterionic glycine. Can you please advise how to fix this problem?

Page: [1]

Re: Glycine optimization ( No.1 )

Date: 2025/01/30 21:24
Name: T. Ozaki

Hi,

You performed the optimization in gas phase.
Are there any previous studies using GGA-PBE, which reported the zwitterionic form of glycine in gas phase?
A theoretical study
https://doi.org/10.1016/0009-2614(92)80116-S
reported that the glycine zwitterion does not exist in the gas phase.

Regards,

TO

Re: Glycine optimization ( No.2 )

Date: 2025/02/01 01:28
Name: dena <daa58768199@gmail.com>

Hello dear
I did not find any article about studying zwitterionic glycine with DFT, but there is an article about zwitterionic serine that was worked with the Sista code.
https://doi.org/10.1007/s11224-019-01426-6
Did the Sista code perform the calculations in a different phase?

thanks.

Re: Glycine optimization ( No.3 )

Date: 2025/02/01 02:36
Name: dena <daa58768199@gmail.com>

Hello dear, is it possible to send the name of the article * https://doi.org/10.1016/0009-2614*?

Re: Glycine optimization ( No.4 )

Date: 2025/02/01 22:43
Name: T. Ozaki

Hi,

The paper is
https://doi.org/10.1016/0009-2614(92)80116-S
"The glycine zwitterion does not exist in the gas phase: results from a detailed ab initio electronic structure study"
Yanbo Ding and Karsten Krogh-Jespersen

Regards,

TO

Re: Glycine optimization ( No.5 )

Date: 2025/02/02 05:58
Name: Dena <Daa58768199@gmail.com>

Thanks alot

Re: Glycine optimization ( No.6 )

Date: 2025/02/06 00:54
Name: dena <daa58768199@gmail.com>

Hello dear
I read the article you introduced. But in other articles, for example,https://doi.org/10.1007/s11224-019-01426-6, the zwitterion state of amino acids is used. This has confused me. Is it possible that with the advancement of functions used in calculations, the ability to calculate zwitterion amino acids has emerged?
Thanks

Re: Glycine optimization ( No.7 )

Date: 2025/02/06 09:26
Name: T. Ozaki

Hi,

The paper you suggested is about serine interacting with pristine and defected CNT, not glycine in an isolated form.
GGA-PBE was uded in the the method, and one can expect that results by OpenMX might be almost equivalent to those
if the same systems are calculated with proper computational settings for both the cases.

Regards,

TO

Re: Glycine optimization ( No.8 )

Date: 2025/02/07 14:44
Name: dena <daa58768199@gmail.com>

Hello dear
Yes, you are right. But since the amino acid used in the article is zwitterion amino acid, it confused me. Thank you very much for your attention.

Page: [1]