Hi
I have optimized a metal ion hydrated cluster in gas phase with 28 atoms. I wolud like to put charge on the metal ion. How to include it in the INCAR file.
I would like to reoptimize the cluster in VASP using MD mode.
I nee 298 K temperature. How to set it in INCAR file?
Thanks in advance
Regards
SMA
charge on metal ion
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charge on metal ion
Last edited by musharaf on Tue Mar 29, 2011 8:59 am, edited 1 time in total.
skmali
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charge on metal ion
Please note that you can only introduce some extra charge to the cell (NELECT flag), not to a particular atom in VASP, due to the PW character of the basis sets.
Please also remind that VASP is based on periodically repeated cells (including the charge)!
concerning dipole corrections for charged cells: please have a look at online manual, chapters Monopole, Dipole and quadrupol corrections, and Dipole corrections for defects in solids.
Please also remind that VASP is based on periodically repeated cells (including the charge)!
concerning dipole corrections for charged cells: please have a look at online manual, chapters Monopole, Dipole and quadrupol corrections, and Dipole corrections for defects in solids.
Last edited by admin on Mon Apr 04, 2011 10:07 am, edited 1 time in total.
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- Location: Mumbai, India
charge on metal ion
The query was like following.
The system we optimized in gas phase was Sr2+-28H2O water clusster of strontium metal ion (charge +2). We took the cartesian coordinates from the optimized geometry and put it into the POSCAR file (see below). Our objective was to see the strutural chnage due to temperature in the system.
The final temperatutre I need 298K. We set IBRION=0 as given in the following INCAR file.
INCAR
PREC = Normal ! standard precision
ISTART=0 ; ICHARG = 2
INIWAV = 1 ; NELM = 60
EDIFF = 1E-5
ISIF = 3
ISMEAR = 0 ; SIGMA = 0.1
IBRION = 0 ! use DIIS algorithm to converge
NELECT = 188
NFREE = 10 ! 2 independent degrees of freedom
NSW =1000 ! 10 ionic steps
TEBEG = 573
POTIM = .5
SMASS=0.4
EDIFFG = -0.02 ! forces smaller 0.02 A/eV
POSCAR
Sr O H
1.000000
20.000000 0.000000 0.000000
0.000000 20.000000 0.000000
0.000000 0.000000 17.000000
1 24 48
Direct
0.492391 0.512450 0.497635
0.517951 0.590942 0.626432
0.508012 0.399517 0.587660
0.420817 0.621082 0.478444
0.393208 0.493491 0.597739
0.556759 0.603937 0.403045
0.397398 0.479260 0.396931
0.542183 0.419386 0.399634
0.619576 0.504437 0.529826
0.663793 0.355101 0.443671
0.272112 0.522557 0.457128
0.464725 0.309292 0.426775
0.571458 0.286742 0.527951
0.387039 0.332226 0.560481
0.371193 0.361809 0.326964
0.389471 0.613110 0.677762
0.280753 0.419055 0.560084
0.512136 0.723419 0.449999
0.299324 0.630103 0.556501
0.503910 0.523691 0.296385
0.684612 0.648985 0.447547
0.738954 0.523811 0.447258
0.744751 0.416910 0.547045
0.599698 0.693559 0.566241
0.581700 0.480347 0.685159
0.463226 0.380902 0.595166
0.533477 0.360239 0.570037
0.513660 0.379263 0.403660
0.586947 0.401895 0.410087
0.353496 0.498134 0.408808
0.386939 0.437127 0.369162
0.351486 0.468373 0.595434
0.385389 0.527698 0.637473
0.659740 0.504466 0.497475
0.634349 0.489446 0.581252
0.543834 0.559699 0.659058
0.549890 0.626061 0.611847
0.543769 0.581312 0.353301
0.604964 0.611198 0.401840
0.376319 0.631053 0.498476
0.441219 0.664666 0.470102
0.692065 0.333423 0.405139
0.695678 0.375851 0.481052
0.235333 0.535118 0.423182
0.277059 0.560726 0.493044
0.499077 0.281989 0.451678
0.434087 0.317395 0.470835
0.609957 0.304154 0.498176
0.589677 0.250627 0.559131
0.345518 0.358122 0.555199
0.372545 0.291329 0.585703
0.366232 0.353483 0.271310
0.403059 0.328226 0.344602
0.388531 0.624336 0.733069
0.437116 0.614481 0.663168
0.269493 0.450114 0.517218
0.238919 0.411316 0.587122
0.508876 0.760396 0.413524
0.528481 0.685114 0.418805
0.325394 0.627241 0.605345
0.272066 0.669676 0.563018
0.457400 0.518685 0.312433
0.522108 0.480592 0.312588
0.705889 0.688964 0.427485
0.662081 0.664199 0.495751
0.730719 0.572086 0.450355
0.749841 0.516591 0.392500
0.760227 0.456999 0.519973
0.784442 0.398105 0.570755
0.567823 0.714326 0.529254
0.612194 0.729552 0.601412
0.593103 0.465007 0.737343
0.553183 0.444989 0.663222
After running it we observe that the wtaer molecule no longer exist as water molecules during MD run. How to run a successful MD for charged hydrated metal ion cluster in VASP will be of great help to us.
Thanks in advance
Regards
SMA
The system we optimized in gas phase was Sr2+-28H2O water clusster of strontium metal ion (charge +2). We took the cartesian coordinates from the optimized geometry and put it into the POSCAR file (see below). Our objective was to see the strutural chnage due to temperature in the system.
The final temperatutre I need 298K. We set IBRION=0 as given in the following INCAR file.
INCAR
PREC = Normal ! standard precision
ISTART=0 ; ICHARG = 2
INIWAV = 1 ; NELM = 60
EDIFF = 1E-5
ISIF = 3
ISMEAR = 0 ; SIGMA = 0.1
IBRION = 0 ! use DIIS algorithm to converge
NELECT = 188
NFREE = 10 ! 2 independent degrees of freedom
NSW =1000 ! 10 ionic steps
TEBEG = 573
POTIM = .5
SMASS=0.4
EDIFFG = -0.02 ! forces smaller 0.02 A/eV
POSCAR
Sr O H
1.000000
20.000000 0.000000 0.000000
0.000000 20.000000 0.000000
0.000000 0.000000 17.000000
1 24 48
Direct
0.492391 0.512450 0.497635
0.517951 0.590942 0.626432
0.508012 0.399517 0.587660
0.420817 0.621082 0.478444
0.393208 0.493491 0.597739
0.556759 0.603937 0.403045
0.397398 0.479260 0.396931
0.542183 0.419386 0.399634
0.619576 0.504437 0.529826
0.663793 0.355101 0.443671
0.272112 0.522557 0.457128
0.464725 0.309292 0.426775
0.571458 0.286742 0.527951
0.387039 0.332226 0.560481
0.371193 0.361809 0.326964
0.389471 0.613110 0.677762
0.280753 0.419055 0.560084
0.512136 0.723419 0.449999
0.299324 0.630103 0.556501
0.503910 0.523691 0.296385
0.684612 0.648985 0.447547
0.738954 0.523811 0.447258
0.744751 0.416910 0.547045
0.599698 0.693559 0.566241
0.581700 0.480347 0.685159
0.463226 0.380902 0.595166
0.533477 0.360239 0.570037
0.513660 0.379263 0.403660
0.586947 0.401895 0.410087
0.353496 0.498134 0.408808
0.386939 0.437127 0.369162
0.351486 0.468373 0.595434
0.385389 0.527698 0.637473
0.659740 0.504466 0.497475
0.634349 0.489446 0.581252
0.543834 0.559699 0.659058
0.549890 0.626061 0.611847
0.543769 0.581312 0.353301
0.604964 0.611198 0.401840
0.376319 0.631053 0.498476
0.441219 0.664666 0.470102
0.692065 0.333423 0.405139
0.695678 0.375851 0.481052
0.235333 0.535118 0.423182
0.277059 0.560726 0.493044
0.499077 0.281989 0.451678
0.434087 0.317395 0.470835
0.609957 0.304154 0.498176
0.589677 0.250627 0.559131
0.345518 0.358122 0.555199
0.372545 0.291329 0.585703
0.366232 0.353483 0.271310
0.403059 0.328226 0.344602
0.388531 0.624336 0.733069
0.437116 0.614481 0.663168
0.269493 0.450114 0.517218
0.238919 0.411316 0.587122
0.508876 0.760396 0.413524
0.528481 0.685114 0.418805
0.325394 0.627241 0.605345
0.272066 0.669676 0.563018
0.457400 0.518685 0.312433
0.522108 0.480592 0.312588
0.705889 0.688964 0.427485
0.662081 0.664199 0.495751
0.730719 0.572086 0.450355
0.749841 0.516591 0.392500
0.760227 0.456999 0.519973
0.784442 0.398105 0.570755
0.567823 0.714326 0.529254
0.612194 0.729552 0.601412
0.593103 0.465007 0.737343
0.553183 0.444989 0.663222
After running it we observe that the wtaer molecule no longer exist as water molecules during MD run. How to run a successful MD for charged hydrated metal ion cluster in VASP will be of great help to us.
Thanks in advance
Regards
SMA
Last edited by musharaf on Wed Apr 06, 2011 6:02 am, edited 1 time in total.
skmali