- Yusuke Tamura added an answer:17How effective are the optimization (and sadpoint) searchs with solvent effects to give good results compared to the vacuum models?
Hello there noble science people...
i am doing equilibrium geometries and saddle point searchs in gaseous phases. but the experiments in which the mechanism were based, used polar solvent and the substances involved were charged particles (although closed shell species).
does this mean i have to emulate these solvent effects for better elucidation and results ? or it'll just make calculation more expensive with little positive gain.
if so,,, is the PCM compatible with geometry and sadsearch? or is there any other alternative approach?
Thank you all. Live long and prosper.
If you are using GAMESS current version of Dec 5, 2014, SMD is available in it. Refer the documents, INPUT.DOC (section2. Input Description) and REFS.DOC (section 4. Further Information on GAMESS document page).
I'm not sure whether GAMESS works as same as G09. I'm afraid you have done TS search with PCM in only one shot. The example 'Fluorescence example' given in the page 'http://www.gaussian.com/g_tech/g_ur/k_scrf.htm' shows a multistep procedure.
Let M(GS) and C(GS) be the energy of solute and the cavity energy, respectively. Geometry optimization for searching M(TS) starts, but C(GS) keeps unchanged. Then optimization of C(TS) is needed until SCF is achieved for both M(TS) and C(TS).?Following
- Anthony Nash added an answer:13How to calculate all the force constants in Gaussian09?When use "opt freq" to calculate water, I only get three frc consts, but the literature had four data. Thanks very much.
I am currently writing some software which will automate this from a Gaussian opt freq calculation. Once I have finished I will point you in its direction.Following
- Oleg B. Gadzhiev added an answer:1What are "good" choices of the active space (CAS) in CASPT2?
I would like to ask for a bit of advice in choosing a "good" active space (CAS) in my CASPT2 calculations for the following reaction:
TiCl4 <=> TiCl3 + Cl
My goal is to obtain an accurate potential energy surface for this reaction (there is no transition state). I did an initial molecular orbital (MO) analysis by hand using group theory and then I confirmed the results by running a simple HF calculations with the double-zeta basis set (vdz). In the equilibrium TiCl4 geometry I obtained the following MOs ordered with an increasing energy:
MOs, bonding type Ti AOs Cl AOs
a1 (sigma bonding, Ti: 4s and Cl: 3s,3p)
t2 (sigma bonding, Ti: 3d,4p and Cl: 3p)
e (pi bonding, Ti: 3d and Cl: 3p)
t2 (pi bonding, Ti: 4p,3d and Cl: 3p)
t1 (non bonding, Cl: 3p) HOMO
e* (pi) LUMO
I am now just wondering which orbitals I should set as active in my MCSCF calculations. I am planning to run a lot of single point CASPT2 jobs, so if possible I would prefer the CAS which is not too big. I am using MOLPRO for all my computations.
I would be very grateful for any advice.
- Rohan Weerasooriya added an answer:21A gaussian error "error in internal coordinate system" when I was doing qst3 jobs.My project is to calculate the transition states for the alkylation reactions of diols through the organotin intermediates. When I did the qst3 jobs using DFT methods to locate the ts, the output files failed with the same reason" Berny optimization.
NTrRot= -1 NTRed= 163 NAtoms= 23 NSkip= 100 IsLin=F
Error in internal coordinate system.
Error termination via Lnk1e in /usr/local/gaussian/g09/l103.exe at Tue Feb 12 15:32:44 2013.
Job cpu time: 0 days 0 hours 4 minutes 8.3 seconds.
File lengths (MBytes): RWF= 60 Int= 0 D2E= 0 Chk= 8 Scr= 1
Does anyone know how to solve this problem?
try introducing a dummy atom, in gaussian09 it is X. and try re-unFollowing
- Christof Haettig added an answer:2How to compile CUDA libraries in turbomole? May I run turbomole using GPU NVIDIA GTX 750 Ti?I was running the QM/MM simulation for the system 216 atoms but 100 steps of configurations needed about 10 hours. I would like to speed up the running. Can anyone give some advice?
If you tell me which version of the source you have I might be able to help you.Following
- Christian Urban added an answer:2Why is the fringe of the STM image is always higher when scanning SrRuO3?
I am doing STM with cleavage SrRuO3.I prepared the STM tip through scanning Cu film and Si(7×7) separately，and the image is fine and can see Si(7×7) clearly. So I think that I have prepared the tip，but when I change the sample to SrRuO3 to scan it，the quality of the image is poor and the left edge of the forward imaging is always high. It is weired! What the reason of this? Can you help me if you have any idears?
I agree with Konrad, the "bad metal" character of SrRuO3 makes it more difficult to have a high tunnel current. The Si is much better for that. So you have to find different conditions for the SrRuO3. That means you have to play with the voltage a lot, change the tunnel current to small currents and apply voltage peaks in between to clean the tip. Dont scan to small, it helps to clean the tip also if you scan very large images for 1h or so, like 5000Ax5000A. Then go back to 1000Ax1000A or so, scan with low currents and high voltage applying 9V voltage bursts for a second or so and repeat that on different areas a lot. It can take days on the same sample to find the perfect conditions. It also might be in the end that the SrRuO3 surface is simple not very smooth but you have to try. Dont give up! Good luck!Following
- Nazanin Molaei added an answer:5How do I calculate molecular orbital density using Gaussian?
Is there any way to account for the sigma and PI molecular orbital electron density separately in a molecule. I am not looking into the graphical abstract information which can be generated using GaussView. Instead, the number which represents the electron densities at an arbitrary grid point in the molecule.
Thanks in advance,
by using this command line # B3LYP/6-31G*opt .Following
- Ricky Singh added an answer:6How might I get optimized structure using ONIOM (QM/MM) method with electronic embedding (EE)?
I would like to perform a geometry optimization using ONIOM (QM/MM) method and electronic embedding (EE). To achieve convergence I have first optimized my system using mechanical embedding (ME). The ME optimization terminated normally. Then I tried to optimize the geometry with the same method but with electronic embedding (EE). I am encountering the following error: ONIOM: Microiterations cycle 26 out of a maximum of 25 Maximum number of microiterations cycles exceeded! Terminating job.
Thanks Venkatesan for that i will have a read.Following
- Atanu Acharya added an answer:6How do you calculate partial charges of an organic molecule?
I have to calculate partial charges for an organic molecule. I have tried to use nwchem to do that but I do not know how to be sure that the partial charges are correct.
My input for nwchem:
geometry units angstroms point xyz autosym
* library 6-31G*
task dft optimize
To add to what Soumyo said,NBO analysis would be most accurate one for the study of organic reaction. The reason being, NBO charges are least sensitive to the number of basis functions you use in your calculation.Following
- Morteza Jamshidi added an answer:22Can we compute fluorescence spectrum of molecules like UV-Visible spectra, NMR and IR spectra?Spectra calculation
you can use the gaussian package , you should optimize structure with td-csf methodFollowing
- Bruno Cramer added an answer:12Any thoughts about the accuracy of Gaussian Composite methods (G1,G2,G3,G4) when applied to calculation of ionization potential of TM complexes?I'm thinking of using high level ab initio methods in calculating the ionization energy of first row transition metal complex. I am also concerned by the possible computational resources that would be required to carry out such calculation. Say, one have only an access to an HPC not a supercomputer. How realistic or practical would this be? And are there any free software package that is equipped with this method?
I recommend that you read the article "A study of the rotational barriers for some organic compounds using the G3 and G3CEP theories"-J Mol Model (2014) 20:2199.Douglas Henrique Pereira et al.
Maybe this approach meets your task requiring less computational cost. With the method G3CEP they got 1.29 kcal.mol-1 deviation against 1.16 kcal.mol-1 deviation with the G3 method. The study contemplates enthalpy of formation, atomization
energy, electron affinity, ionization potential, and proton affinity. Computational costs were reduced from 7% to 70% depending on the molecule's size.
Try the method out repeting the procedure with a couple of molecules so you get some feeling about it in order to proceed with the method or not. Good luck.
- Apurba Bhattacharjee added an answer:2What is the best way to find the most stable disulfide bonds of substructures in a higher-order structure?
I want to create a higher-order structure of a designated substructure (see Figure). Along the edges of the octahedron, I would like to link the trimers with disulfide bonds (potentially with other interactions). Is there any good (computational) method to calculate which amino acid would best be replaced by cysteine to form the most stable disulfide bonds? I used Chimera for this model so far but I'm open for other programs.
My guess is that you may need to perform ab initio quantum chemical calculations of the substructure using higher levels of theory (DFT calculation). You may try first with RHF/6-31G(d,p) level followed by further higher levels to find out consistency of the bond lengths .Following
- Imre Tóth added an answer:6How do I find the transition state of CO insertion to 1-dodecene on a Rh(I) catalyst?
Hello, I am trying to find the transition state of the CO insertion to dodecane on a Rh(I) catalyst. I can not find the transition state and I think it's because my initial structure is not good enough. I am using DFT-BP86 RI with def-SV(P) basis set. According to the mechanism I have CO coordinates first to Rhodium and then it should some how migrate to the alkane. The end product should be tridecanal attached to Rhodium. So what could be an initial structure to use and are the level of theory and the basis set suitable?
SCF energy convergence parameter 10^-6
One more important aspect of the insertion and elimination mechanisms that they are likely to occur from a planar cis-position instead of others, including apically placed groups. In your case CO insertion is unlikely from a species, where either CO or the alkyl group is apically placed. In these cases an appropriate rearrangement is required in the complex structure.Following
- Anji BABU Kapakayala added an answer:5What are the inputs for the following INCAR files?I need to optimize the Zn doped TiO2 (101) surface using DFT+U. I would like to know the input for INCAR files. Thank you.
In above case LDAUL = 2 -1 , Here L is the Quantum number for which onsite intraction is added.
In above case TiO2, Ti is magneteic so we need to add onsite intractions to Ti ie 2, where as for O no need to add so L= -1.
"L is just switching operator on which atom we need to add onsite intractions, it is either 2 or -1( On=2, Off=-1)"
- Gediminas Baltulionis added an answer:4Any advice in finding different thermally adapted protein homologs?
Can someone suggest the best route of finding protein homologs from thermally adapted subsets of proteins? For example, if I am looking for homologs only within psychrophilic/mesophilic/thermophilic proteins?
Thank you for informative answers. In my case I am trying to increase the thermolability for the protein. Thus I am looking for psychrophilic structural/functional homologs.
Chris good point about selecting for more stable mutants using Yeast Display, but I am not sure how this would work for less stable mutants.
- T. P M Goumans added an answer:16Are there instances that theoretical search of a TST is impossible even if experiment suggests it exist (LFER) for some "very concerted" reactions?
I've been calculating and searching a TST structure of this "Sn2 concerted reaction" (as suggested by experiment through LFER) for months
the experimental energy barrier is about 21kcal/mol which rather small
my first initial runs involves minimization (optimization) calculation showed that the nucleophile is really attacking the center and the simultaneous detaching of the leaving group...from frame 1 to the end, IT SUGGESTS THAT SN2 reaction really happens...
but when I chose some frames in THE CRUCIAL POINTS (NSERCHS) of the attack and subject it to SADPOINT searches.. THe search goes to the product side as if the reaction is fast that the TST is very difficult to catch...
another thing is that frequencies of this frames that I examine contains very small imaginary values as if it is stable which is contradictory...
Im using DFT and MP2 for these searches using appropriate basis sets for the system which were based on the previous studies)...
Can anyone enlighten me with Localization of TST in concerted reactions with small energy barriers...
- Manish Sharma added an answer:11Is their any software to view phonon modes obtained from calculation in Quantum espresso (Phonon.out or dynamt.out)??
Even after following a very strict convergence criteria for SCF and Ph.X calculations I am getting some imaginary frequencies. I just wish to find out which all vibrations are causing these imaginary frequency to occur.
Thanks a ton Vaibhav, thats exactly what I was looking for :).Following
- Javier Cerezo added an answer:7What is the UV-spectrum of beta-carotene on Gaussian 03?
I have been attempting to calculate the UV-visible spectrum of beta-carotene using Gaussian 03 at a level of theory of TD-DFT/B3LYP/6-31g (on a pre-optimized structure). The spectra obtained for beta-carotene experimentally have characteristic shoulder peaks at 450-470 nm. However when I do the calculation, I don't get these peaks, only one peak at about 470 nm.
Could anyone help me out with why this might be? Is there an error in my methodology?
In the case of beta-carotene and carotenoids of similar size, the bright broad band is assigned experimentally to the S0->S2 transition. The state S2 is characterized by a HOMO->LUMO character and it is normally the one corresponding to the first root in TDDFT. S1 state has multireference character and one would need to go beyond DFT (CASSCF, MRCI...) to catch it properly (e.g. Chem. Phys. 373 (2010) 98-103) but since S0->S1 is not allowed in one-photon absorption, this is not a problem to get the spectrum.
A single point TDDFT calculation would give you the vertical energy, i.e., a single line which is normally convoluted with a Gaussian to get an approximation of the spectrum. Depending on your goal, that can be good, and you should focus on finding a DFT functional that provides you with an accurate prediction of the vertical energy. As pointed out by Ignat Harczuk, at this point, the inclusion of the solvent is crucial in order to get a realistic estimation of the vertical energy.
However, as stated along this post, if you want to get the fine details of the band, you need to incorporate the vibrational structure. As pointed out by Bojidarka B. Ivanova FCclasses is a very good tool to do it. However, note that beta-carotene is a challenging system due to:
1. The size of the system: this implies that the optimization and, mainly, the computation of the frequencies on the excited state is quite expensive. But with patient and enough computational resources, this can be solved. Note that it would also be preferable that the optimization/frequency calculation is done incorporating the effect of the solvent.
2. There are a lot of vibrational states, which implies that to get the vibrational shape you need to account for an extremely large number of vibrational transitions with TI methods. Moreover, since a lot of the modes have low energy, a lot of vibrational states of S0 will be populated at room temperature, which further increases the number of possible vibronic transitions. Indeed, the experimental spectrum already shows a very remarkable temperature effect (experiments at 77K and room temperature are available in the literature, and they are quite different). The best solution is going for a TD method (instead of TI), which do not need to compute the vibrational states, but rather compute the dipole correlation function, which is analytical in the harmonic approximation (J Chem Phys, 119 (2003) 7188-7196; Chem. Phys, 370 (2010) 215-222) (but you still need the frequencies).
3. For beta-carotene, the optimized structures in the S0 and S2 states reflect a large structural displacement concerning the dihedral that connects the beta-ionone ring with the conjugated chain. This challenges the description of normal modes in Cartesian coordinates and, indeed, it has been shown that one would need to go to internal coordinates (J Chem Phys, 115 (2001) 9103-9109) or use vertical approaches to perform a realistic simulation of the spectral lineshape of this molecule (J. Chem. Theory Comput. 9 (2013) 4947-4958)Following
- Saleh Alarfaji added an answer:21What would be the problem if the Gaussian frequency calculation stops after calculating the rotational constant?
I am trying to calculate the frequency of a transition state of the molecule, but everytime the running jobs stops after calculating the rotational constant in the output file and shows" Error termination request processed by link 9999."
I would be very thankful if anyone could help me with the reason of this problem and what can be done?
I already tried increasing the SCF Maxcycle, but it still got struck at the same point mentioned above.
Make sure you have started with good initial parameters and try to use opt=CalcFC with a low level of theory first. Hope that will help.Following
- Henk Smid added an answer:8Is there any experimetal data for terminal velociy of alkans falling droplet in air?
I need experimental data for terminal velocity of Hexene/Hexane/similar alkanes falling droplet in air to validate my numerical scheme. In brief, I want to know if there is any data for droplets with density ratio less than water droplet in air. can anyone introduce any related work?
Dear Ahad Zarghami,
In the study of a falling droplet, there are a lot of effects that should be taken into account (ideally). Stokes' Law is usually applied but with all kind of 'fudge-factors'.
The gas the droplet is falling through is not a mathematical ideal fluid. The form of the droplet is not spherical and, unfortunately, depends on the resisting medium. (The shape probably is not even constant.) There are more things you can think of how the real system differs from the ideal.
However, all those effects can be caught in a small number of 'effective' parameters. that of course depend on the actual system at hand.
What I meant with scaling laws was merely that those effective parameters usually depend on a similarly small number of macroscopic quantities. Think of: the density of the gas, the density and average radius of the droplet...
If you are interested in a particular system, you could look up systems 'close' to yours and scale your parameters.
But , then again, that wás your initial question. So, I was not of great help.
Kindest, Henk SmidFollowing
- Quang Thang Trinh added an answer:1Any advice about DOS at the interface of p-n junction?
Dear Researchgate community members,
I have a question regarding physics. We tried to do a calculation for an organic(p-type)-inorganic(n-type) interface for p-n junction photodiode. First we did a calculation for organic part, then the inorganic part and finally both together. All three of them were performed for the same unitcell size.
But while plotting DOS for the interface, the organic donor [p-type](as reported in literature) DOS shifts to lower energy, making it n-type.
I do not know where is the problem. Some literature suggests that part of the DOS (organic part) need to be shifted with respect to the vacuum level. How to do that?
I will be highly obliged if you can kindly give me your suggestions regarding this.
Thank you very much, with kind regards,
Thao P Nguyen
P.S. See the attachment.
Hi, if you are analyzing DOS by VASP, you can specified the atom that you want to consider (here are the atom staying at the interface. For this purpose, you should generate the POTCAR (pseudopotential) and POSCAR (position) correspondingly. Then you might be able to see the electron transfer in the interface zone. If you do not specify those interface atom, you will get the DOS for the whole system.Following
- Elvis A. F. Martis added an answer:2How can I construct a supercell from a single molecule?
I am trying to construct a supercell using GDIS. When I laod the pdb file then go to the option of making the supercell then this option is freezed and i cannot add aotms more atoms to make super cell. Is there any problem with my molecule or of the software.(I am using GDIS 0.90 in Linux)
Perhaps you can use UCSF chimera.
Go to Tools>higher order structure.
Hope this helpful to you.
All the bestFollowing
- Vaibhav Kaware added an answer:1How do I solve my CI-NEB middle image convergence problem?
I was doing a CI-NEB calculation using VASP together with VTST code as per mentioned http://theory.cm.utexas.edu/vtsttools/neb.html.
The problem I am facing is the following.
Irrespective of the middle image being a saddle point or not, the forces on the ions on this image do not converge where as in all other images, every thing looks fine. And I could not figure out why...
to be specific, i am using LDA as EX-fucntionals and my INCAR is posted in here in the following:
SYSTEM = NEB-YSZ
ISYM = 0 # switch off symmetry
Start parameter for this Run:
ISTART = 0
ICHARG = 2
NELM = 100 # max number of electronic SC steps
NELMIN = 5 # no of min of electronic SC steps
NELMDL = -10 # no of non-SC steps at the begining if ISTART = 0
Electronic Relaxation 1
ENCUT = 500 eV
IALGO = 38
EDIFF = 1.0E-6
# NELMIN = 5
EDIFFG = -1.0E-3
NSW = 500
DOS related values:
ISMEAR = 0
SIGMA = 0.05
Cell Volume + Cell shape
ISIF = 3
Other Calculation parameters
PREC = ACCURATE # Advised to do so
LREAL = .FALSE.
LWAVE = .FALSE.
LCHARG = .FALSE
IMAGES = 7 # Number of NEB images between the fixed endpoints
SPRING = -5.0 # The spring constant, in eV/Ang^2 between the images; negative value turns on nudging
ICHAIN = 0 # Indicates which method to run. NEB (ICHAIN=0) is the default
LCLIMB = .TRUE. # Flag to turn on the climbing image algorithm
LNEBCELL = .TRUE. # Flag to turn on SS-NEB. Used with ISIF=3 and IOPT=3
# Must set IOPT = 3 or 7 when using LNEBCELL=.TRUE.
IOPT = 3 # QM (Quick-Min) force based optimizers is used and good for high force far from minmum
# O(default vasp),1(LBFGS),2(CG),4(SD),7(FIRE)
IBRION = 3 # Disbale VASP default optimizers which are basesd on Energy
POTIM = 0 # Disbale VASP default optimizers which are basesd on Energy
#MAXMOVE = 0.2 # Maximum allowed step size for translation(Default comes with IOPT=3)
TIMESTEP = 0.1 # Dynamical time step (Default comes with IOPT=3)
LSCALAPACK = .FALSE.
NPAR = 4
I am looking forward to hearing from any one.
Since NEB samples the potential energy surface (PES) only at specific points, it is possible that your middle image is surrounded by real complicated PES. My first suggestion in which case would be to try if anything changes by increasing the number of images in the NEB.
Did you try to watch the movie of the resulting MEP? What do you see?Following
- Karuppusamy Masiyappan added an answer:5Can anyone help with this Gaussian error message- "write error in NtrEx1"?An error message " write error in NtrEx1" is showing when I was doing optimization and frequency calculation in Gaussian 09. Can anyone help me?
based on my experience, obviously its from memory related error only. Give the memory values in MW(MegaWords) instead of GB and MB. Ans also clean your scratch files. I hope it will be helpful to you.Following
- Pritam Kumar Panda added an answer:5Which is the best, precise and inexpensive method for theoretical docking studies on protein ?
I am interested to study a ligand-protein interactions via computational chemistry. I was told to use MGL Tools 1.5.6 ( with autodock 4 and autogrid 4 ) followed by CYGWIN to complete the process on a Windows operating system.
I find using CYGWIN bit confusing !
Can anyone suggest inexpensive alternative methods or corrections to the above procedure for the study.
Do with Autoock Vina, a command based program for molecular docking studies. Results can be analysed using Discovery studio Visualizer 4.1 which is freely available in Accelyrs Website. Even you can also analyse the post docking analysis in Autodock itself defining a cutoff range to visualise the interaction (H-Bonds).
- Bhawana Pandey added an answer:3Which basis set is good for Tellurium (Te)?Basis set for Te for DFT calculations?
- Zeinab Abde added an answer:7Can anyone help with an error termination about Gaussian 09 calculation?
I am trying to find out the structure of a transition state
for a decomposition reaction (HXeXeF→HXeF+Xe) by using QST3 and I get the following error:
Inconsistency: ModMin= 2 Eigenvalue= 1.54137914D-03.
Error termination via Lnk1e in /usr/share/apps/g09/l103.exe
Does anyone have an idea of what this means and how to solve it?
Dear all, thank you for your responds.Following
- Karteek K. Bejagam added an answer:2How can I calculate storage and loss modulus from molecular dynamics simulations?
I learned by doing Fourier transform of stress auto-correlation will give the modulus. But getting into the trouble with the bin size.
dw = 2*pi/ Time and to achieve points in 10^-4 region, performing the simulations for long duration is not possible. Can anyone help me out in this regard?
I am interested to obtain via writing a stress-stress correlation and taking a Fourier transform of it to get storage and bulk modulus.Following
- Thomas Schied added an answer:5How do we compute the density profile in terms of the z-axis coordinate and the cylindrical radial coordinate r?
I am trying to compute the normalized density profile in terms of the z-axis coordinate and the cylindrical radial coordinate r of solvents from the centre of mass of a rigid body. How can be generate a histogram for density at a given (z, r) averaged over all azimuthal angles? Please explain the algorithm for binning.
perhaps you can post some kind of drawing, as I am also having some trouble understanding your problem.Following
- Laura Ingersol added an answer:6Why are my orbital energies in Avogadro all the same?
I ran an optimization job on a transition metal complex in Gaussian using ground state DFT, B3LYP, LanL2DZ. It converged, but when I opened the fchk file in Avogadro, while the orbitals are displayed correctly, the energies are not. Using the extensions->molecular mechanics->calculate energy on each individual orbital gave me the same energy for every one, which is impossible.
I checked the log file, but I am not seeing the energies. Is this a problem with my input?
What units do these values have in Gaussian?Following