Computational Chemistry

Computational Chemistry

  • Shobeir K. S. Mazinani added an answer:
    What is an appropriate method to explicitly solvate a solute prior to ab initio optimisation using Gaussian?

    I have a compound, which we expect interacts with water. Experimentally the level of hydration in a tissue samples changes upon including this compound. We aren't exactly sure, though, how (if) water molecules are non-covalently interacting with the compound. We have identified four different sites which are very polar in nature. I wish to get the relative energy (relative to the unbound state of the compound) of water binding using 8, 10, 12, and 14 explicit water molecules using Gaussian. I have based these number on a number of studies on the hydration of aldehydes.

    I have a good geometry of the compound (optimised separate). I want to:

    a) identify the key water binding group (so a separate relative energy calculation per potential binding group),

    b) calculate the relative energy of a totally immersed compound i.e., explicit water molecules around the 4 potential sites (obviously depending on (a)).

    I am struggling though to justify (I have none) the position of the water molecules around each key site in my initial geometry. What would be the best technique? I have tried an energy minimisation using a Universal ForceField (UFF), but depending on the water molecule orientation this can separate molecules well over 2.5 Angs apart.

    Is this a case where I should try constructing the possible hydrogen bond network (water-water-compoundgroup) by hand?

    Finally, would it make more sense to model this in a vacuum, rather than an accompanying implicit water model? I am concerned that an implicit water molecule could interfere with intermolecular hydrogen bonds between water-water and water-compound.

    Many thanks

    Anthony 

    Shobeir K. S. Mazinani · Arizona State University

    Dear Anthony,

    I agree with others in that it is good to have an MD calculation as a starting point and use between 5 to 10 systems as your initial point. I believe adding the implicit water (continuum models) is essential. From my experience in simulating NMR and EPR parameters and also trying to correlate the orbital energies with some observables, it is normally necessary to add both implicit and explicit models simultaneously.

  • Yin Li added an answer:
    How to define a crystal structure in quantum-espresso (pwscf)?

    In the tutorial of quantum-espresso (pwscf), the tutor demonstrated how to set up a unit cell using the parameters list below.

    ibrav=2,

    nat=1,

    ntyp=1

    Only 1 atom is enough to define this face-centered cubic. As far as I understand from this parameter, the software will know where to place 14 atoms in one cubic (8 corners and 6 face centers).

    However, I was confused by the second example. The tutor only used 2 atoms to define a diamond structure (Fig 1).

    ibrav=2,

    nat=2,

    ntyp=1

    Atomic_position

    Si 0.0 0.0 0.0

    Si 0.25 0.25 0.25

    If the first Si was considered as the atoms whom should be placed in the 8 corners and 6 face centers in one cubic, how does the software know where to place the second Si? How does the software distinguish the diamond structure from fluorite structure (Fig2)?

    Yin Li · University of Pécs

    Thanks, Vaibhav! I will try it.

  • Adam Kubas added an answer:
    What do you think about recent JCTC paper of Truhlar et al. about benchmarking DFT against CC for TM complexes?

    Hi All,

    I have just read very recent paper "Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals?" by Xuefei Xu, Wenjing Zhang, Mingsheng Tang and Donald Truhlar published in JCTC ("just accepted"). Here is the link:

    http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00081

    They looked how few DFT functionals perform for the dissociation energies of a set of diatomic, transition metal-containing molecules and compared this to the performance of a hierarchy of CC approximations (CCSD, CCSD(T), CCSDT, CCSDT(Q)). They concluded that CC, although much more elaborate and time consuming, are not better than modern DFT functionals. They also questioned benchmarks of DFT methods against CC for TM systems. 

    With the results they presented the conclusions are right. Of course, as they properly noted, if the experimental data change the trends can also be changed. As I'm personally interested in TM compounds and do a lot of calculations on these systems (DFT, single- and multireference wavefunction-based methods), I'm quite surprise that they make such strong statements. 

    First of all, I would never use CC methods for the molecules in question. Multireference treatment would be preferred. Linear molecules tend to have near-degenerate states. Most of the complexes we deal in real life have stronger ligands and way lower symmetry and consequently highly single-reference character. The latter, as properly pointed by authors, is not well defined. In fact, T1, M and B1 diagnostics used in the paper do not seem to correlate between each other. 

    In larger systems weak interactions tend to have really large impact and consistent solution for this problem is still not definitely done in DFT. The DFT errors here can reach more than deviations presented in the paper.

    Although the paper is very solid, I'm a bit sceptical about the generality of conclusions made. I would be curious to hear your feelings about this paper and about benchmarks for transition metals in general. 

    All the best,

    Adam

    Adam Kubas · Max Planck Institute for Chemical Energy Conversion

    Indeed, the basis set incompleteness error (BSIE) in DFT and CC is rather different. Probably the authors just wanted to use a typical protocol people would follow when benchmarking DFT, i.e. DFT with reasonable basis set (typically of TZ quality) and CCSD(+some treatment of T, rarely Q) with moderate basis set. However, if you can afford calculations like in the paper, then next step would be something that accounts for BSIE. One typically takes two point extrapolation, corrects with MP2/CBS or uses F12 approach. I just think it is unfair to stop at the level they done.

    DFT has larger error spread and this would be quicker visible from RMS error, I agree. Probably one should always provide as much statistics as possible to avoid overinterpretation :)

    I also do think that benchmarking with CC methods for TM compounds still has bright future because:

    1) many complexes/reactions are still single-reference problems,

    2) if 1) is not true then use MR-CC and if impossible then MRCI, NEVPT2, CASPT2 etc. At this point do not expect that DFT will do the job either. You can just be lucky.

    3) whenever possible go to CBS. There are various ways to do so.

    4) points 1-3 become more and more feasible with locally correlated methods, efficient parallel computing etc. we will definitely see explosion of wave function based results in the nearest future!

  • Bojidarka B. Ivanova added an answer:
    How do I obtain geometries of S1 excited states from Gaussian09?

    Hello,

    I am trying to get optimised geometries of brominated benzenes from Gaussian09 using CIS and TD methods. Both gives unexpected shoter C-Br bond lengths (around 1.86 A), even shorter than bond corresponding distances in the ground state (around 1.9 A) , Experimentally, bromobenzene degrade by loss of Br via photo-induced decomposition so shortening the C-Br bonds in the optimised first excited state, in reference to the ground state is not what you would expect.

    If I use the newly added optics feature to Dmol3 to carry out optimisations for the first excited S1 state, the C-Br distances are elongated to 2.10 A which makes a sense.   Turbomole gives similar results.  I am just wondering if any one has experienced similar situation when using G09 to option geometries for halogenated hydrocarbons in the excited state.

    Bojidarka B. Ivanova · Technische Universität Dortmund

    Mr. Altarawneh,

    You have received this deviation, because of most probably you have not performed a preliminary optimization of the geometry in ground state.

    Please find as attachment an example of CH3Br. First, the geometry have been computed at a given suitable level of theory, and afterward this geometry has been used as initial one to obtain excited state properties.  

  • P. V. Vladimirov added an answer:
    Are the phase field modeling methods applicable to non-equilibrium problems?

    The basis for the phase field modeling is minimization of a functional presenting some thermodynamic potential (e.g., free energy), which is conserved in the system considered. Therefore, time evolution of the system described by the phase field is not the real kinetics, but just some pathway the system proceeds to the equilibrium state.

    It is like using the Metropolis Monte Carlo for minimization of the energy of a system. The final state might correspond to some local or global minimum, but the way the system relaxes to it is not the real kinetics. The real kinetic pathway should be described by the kinetic Monte Carlo approach.

    Therefore, the question of applicability of the phase field methods to non-equilibrium problems arises. Are these methods applicable for micro-structure evolution under irradiation?

    I am aware about the large number of publications on the void and gas bubble growth under irradiation. However, I am interested in justification of this approach from the ground principles, not just "use it because the others do so".

    I would enjoy discussion on the topic, many thanks for your replies.

    P. V. Vladimirov · Karlsruhe Institute of Technology

     Thank you all for the clarifications.

    As far as I understood, despite of the lack of equilibrium in the case of void and bubble growth under irradiation, the phase field methods are well applicable to the second order phase transitions, but their applicability to the first order transitions is less grounded.

  • Muhammad Khattab added an answer:
    How to use the output of low level of theory calculation, as input for a higher level of theory, in details please?

    i read that i can use the checkpoint file of low level method to save time and getting a better accuracy.

    Muhammad Khattab · National Research Center, Egypt

    Thanks you all!

  • Joaquim Mª Rius Bartra added an answer:
    Why B3LYP was not re-optimized?

    When I was studying adiabatic methods (hybrids) the first to apply three parameters to correlation integral was Perdew, giving the B3PW91. Later, it was suggested to apply full correlation method (LYP) but the three parameters optimized was not change to fit to LYP and giving the B3LYP without new optimization.

    Could be this change give extra errors in systems more complex than organic ones? This is the reason that B3PW91 give better results for metals than B3LYP?

    Thank you very much.

    Joaquim Maria Rius Bartra

    4th Grade Chemistry.

    Universitat Autònoma de Barcelona

    Joaquim Mª Rius Bartra · Autonomous University of Barcelona

    Thank you very much for all explanation, it is very clear.

  • Kaveh Haghighi Mood added an answer:
    Help for GAMESS Calculation?

    Calculation on Beryllium: ndoc=2 nval=2

    Why does it say 4 occupied out of 5 MOs?

    Kaveh Haghighi Mood · RWTH Aachen University

    Hi

    What is your spin multiplicity, charge and  term symbol? basis set?

    Your input means you have 4 active orbitals with 4 electrons. 

  • Mohsen El-Tahawy added an answer:
    Can anyone explain how I can calculate the polarizability from the molcas CASSCF output calculation?

    in the molcas output of CASSCF calculations I have the following section of calculation for each state

      ++    Molecular properties:
     
          Charge (e):                     =   -0.0000
          Dipole Moment (Debye):
          Origin of the operator (Ang)=    0.0000    0.0000    0.0000
                         X=   12.5785               Y=   -0.7950               Z=   -3.7798           Total=   13.1582
          Quadrupole Moment (Debye*Ang):
          Origin of the operator (Ang)=   -0.4352   -0.1135    7.2646
                        XX= -176.2855              XY=    6.1575              XZ=  -12.9620              YY= -163.3657
                        YZ=    0.4213              ZZ=  -24.1633
          In traceless form (Debye*Ang)
                        XX=  -82.5210              XY=    9.2363              XZ=  -19.4430              YY=  -63.1413
                        YZ=    0.6319              ZZ=  145.6623
    can I use this data to Calculate the polarizability? How?

    Mohsen El-Tahawy · University of Bologna

    thank you dear Ivan for your hlep

    my molecule is retinal and it is oriented in z-direction (main chain) and I am using FFPT molule to apply the electric filed in this direction. of course I usually do a correction using CASPT2 and it give a similar section of data for each state (I mean Molecular properties section shown in my question ). I will study the paper you have attached. I wonder if I can calculate the alpha-polarizability from this section og out put ORshould I do additional calculations?

  • Eugene F Kislyakov added an answer:
    How do I calculate the Antiferromagnetic coupling energy in Vasp? What are the tags?

    Material Chemistry, Computational Chemistry....

    Eugene F Kislyakov · Belarusian State University

    Naga,

    for what 4 electrons? Is not 2 enough?

  • What does erroneous write stand for?

    Working with silicon two-layered clusters, I get an error message that goes like:

    Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00.
    Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00.
    End of G2Drv F.D. properties file 721 does not exist.
    End of G2Drv F.D. properties file 722 does not exist.
    End of G2Drv F.D. properties file 788 does not exist.
    IDoAtm=11111111111111111111111111111111111111111111111111
    IDoAtm=11111111111111111111111111111111111111111111111111
    IDoAtm=11111111111111111111111111111111111111111111
    Differentiating once with respect to electric field.
    with respect to dipole field.
    Differentiating once with respect to nuclear coordinates.
    CalDSu exits because no D1Ps are significant.
    There are 435 degrees of freedom in the 1st order CPHF. IDoFFX=6 NUNeed= 3.
    435 vectors produced by pass 0 Test12= 1.13D-12 1.00D-09 XBig12= 1.46D+04 1.75D+01.
    AX will form 72 AO Fock derivatives at one time.
    435 vectors produced by pass 1 Test12= 1.13D-12 1.00D-09 XBig12= 6.83D+03 2.12D+00.
    Erroneous write. Write -1 instead of 509295232.
    fd = 4
    orig len = 650011392 left = 509295232
    g_write

    I am using pbe0/6-31G** requesting a freq calc and adding the xqc on the scf, annexed are my files. It's not the first time I get this message for I've adjusted the system several times with no result

    Thanks!

    Best regards

    Juan-Sebastián Gómez-Jeria · University of Chile

    Use the option int=nofofcou and tell me it it worked or not. Regards, Juan

  • Justin Lemkul added an answer:
    Can anyone help me use martinize.py to generate coarse grain structure of a iron pyrite nano cluster?

    I created iron pyrite nanocluster in material studio 7.0 and exported it as .pdb file.

    I downloaded martinize.py to convert this nanocluster to coarse grain and create simultaneously cg.gro and topology file in GROMACS 4.6.5.

    But, the topology file and cg.gro file does not have any coordinates.

    Can anyone help me out how to use martinize.py to generate coarse grain structure of iron pyrite nanocluster?

    Justin Lemkul · University of Maryland, Baltimore

    Parametrizing something like this with a CG force field may not even be possible.  Even atomistic FF fail to describe transition metals adequately.  There are significant quantum effects whenever a transition metal is involved.  A cluster of uncharged CG beads seems likely an inadequate description, in my opinion.  CG representations are fine for mesoscopic phenomena, but in cases like this, I think CG is far less valuable.

  • Rameswar Bhattacharjee added an answer:
    How do I perform EDA (energy decomposition analysis) in G09?

    Is it Possible to do EDA (energy decomposition analysis) using NBO method in G09? I want to use ecp basis for this.It is possible to do in gamess but I dont know hot to use ecp in gamess.Any suggestion will be highly appreciated.Thank you.

    Rameswar Bhattacharjee · Indian Association for the Cultivation of Science

    Thank you all for the valuable suggestion.As Sirous told I can mention basis set for different atoms in gamess input but I am not sure how to specify? In g09 input I can use external basis but in games what will be the format? Suppose If I have a Pt(H2O)6 and I want to use lanl2dz basis set for platinum and 6-31+g(d) for others that how I will write it in the input section of gamess?

  • Salvatore Profeta Jr added an answer:
    Can anyone tell me how to select a basis set 6-31G and not 6-31G* in Spartan?

    Can anyone tell me how to select a basis set 6-31G and not 6-31G* in Spartan. I have an old version of the software and the basis sets with EDF2 is rather fixed. 

    Salvatore Profeta Jr · Florida State University

    Murad,

    I am assuming you are using the full and not the Student version of Spartan. If you go into the Calculations Setup menu, simply type HF 6-31G in the options field. Any basis that you note there will override the basis from the drop down menu. I have pulled the note on this from the SP'14 manual and also output from a job I just ran to verify the Option use.

    Good Luck!

  • Salim Hammani added an answer:
    How do I measure relative crystalinity using OriginPro Lab?

    As we can measure the relative crystallintiy using  ratio of Area under the crystalline peaks to that of scattering from total diffractogram. Now to measure the area under the peaks, should I use integration in Origin or should I use the multiple peaks, as it also gives the area along with other parameters.

    Salim Hammani · Saad Dahlab University

    the question is more general, if you are in the case of the polymer blend: you can use the area of the melting peak instead the cooling phase, if your system is inorganic (in this case I'm very sorry). 

  • Oleg B. Gadzhiev added an answer:
    How much spin contamination is okay in a Stable=opt calculation?

    The reason that we use the stability analysis (on singlets) is to make sure we are actually modeling the ground state of the real system in question, but this also seems like it could be a little bit counter-intuitive because the resulting wavefunction is then spin-contaminated. This is supposed to happen, right? If so, what is a good <S**2> value / rule-of-thumb estimate to expect after a stability reoptimization of the wavefunction?

    Also, this next question is not quite as important, but still worth asking. What does it mean when the spin-projected wavefunction has more spin-contamination than the original? I have only seen this happen once in a singlet calculation of ammonia-coordinated iron(II), but it definitely happened. This is approximately what happened: <S**2> = ~0.8 -> 1.1 after annihilation, for reference.

  • Bojidarka B. Ivanova added an answer:
    What basis and functional set would be suitable for ab initio calculations of copper and zinc ions, an organic compound and water?

    Hi all,

    I'm considering running a handful of explicitly solvated (water) organic compound ab initio calculations in the presence of either a copper or zinc ion. I hope to find whether my compound sequesters the ion in question.  My system is made up of 64 atoms: 6 O, 6 N, 18 C, the rest hydrogens. I aim to solvate between 8 to 16 water molecules, with either a single Zn or Cu. Already this is a relatively big system ab initio wise. 

    I've gone through dozens of manuscripts, all of which report several combinations of different function/basis-set pairs: from B3LYP, MP1-4, wb97xd, HF etc., and lanl2dz, 6-311++g(combination in here), and even DFT-U (which I have no experience with I'm afraid). 

    I understand some basis sets are selected according to what computational resources are at hand, that is to say an explicit split-valence or something with an electron core potential. 

    Any suggestions?

    Many thanks

    Bojidarka B. Ivanova · Technische Universität Dortmund

    Mr. Nash,

    Please find as attachment the accuracy of the discussed methods, including some other ones towards actinides (attachment ref. [1]). As it has been mentioned in this forum, the application of B3PW91 has yielded to generally meaningful results. The accuracy, predicting vibratioal properties is within 1 - 20 cm-1.

    In addition to lanl2dz, I would to add sdd (attachment) as well as the reference [2] shown below, have provided information about the reliability of the data obtained.

    [ref. 2] Lamshoft, M.; Storp, J.; Ivanova, B.; Spiteller, M. (2011)

    Gas-phase CT-stabilized Ag(I) and Zn(II) metal-organic complexes–experimental vs. theoretical study, Polyhedron, 30, 2564

      Particularly ref [2] is on ZnII and AgI complexes. 

  • Bojidarka B. Ivanova added an answer:
    Is there any method to calculate bond dissociation energy through quantum chemical calculations?

    I have a system with around 300 atoms (a disulfide bond in the center). I would like to calculate the bond dissociation energy of this disulfide bond. Is there any method other than excitation, to calculate the bond dissociation energy between the two sulfurs?

    Bojidarka B. Ivanova · Technische Universität Dortmund

    Mr/Mrs/Miss Bhatnagar,

    Please find as attachment the accuracy of some quantum chemical approaches in prediction of De. The book cited (Chapter 4) [1] has contained additional information for both ab initio and DFT methods in the topic of your question, including data about appearance and ionization potentials, because of we have correlated exactly the quantum chemical accuracy with the available experimental mass spetrometric information about the various fragmentation pathways. The thermodynamic parametersof such as processes have been also discussed. 

  • Bojidarka B. Ivanova added an answer:
    What is the difference between AM1 and PM3 methods?

    What is the difference between AM1 and PM3 methods in computational chemistry and when is it better to use one over the other?

    Bojidarka B. Ivanova · Technische Universität Dortmund

    Mr./Miss/Mrs. Albar,

    The formalism is the same, but the parameters are different.
    Please find in this topic the following refs:

    [1] M. Dewar, W. Thiel, Ground States of Molecules. 38. The MNDO Method.
    Approximations and Parameters, J. Am. Chem. Soc. 99 (1977) 4899 - 4907
    [2]M. Dewar, E. Zoebisch, E. Healy, J. Stewart, AM1: A New General Purpose Quantum Mechanical
    Molecular Model, J. Am. Chem. Soc. 107 (1985) 3902 - 3909

    [3] J. Stewart, Optimization of Parameters for Semiempirical Methods
    I. Method, J. Comput. Chem. 10 (1989) 209-220

    In addition you can find their application in vibrational spectroscopy and the correlations obtained for few examples (attachment).

  • Christian Kandt added an answer:
    How is charge group defined in gromos force field when adding new residue to .rtp file? Is there a gromos bond type for the bond between C and OE ?

    I am trying to run MD for fluorescein, a small molecular weight green dye. I need to add a new residue (which exists in pdb file that I created by deleting the rest of the molecule and leaving fluorescein alone) to aminoacids.rtp in order to create a topology file using gromos 53a6 force field. I am having difficulty in modifying the rtp file because I need to define gromos types for bonds, angles, dihedrals and impropers. I found the needed parameters from another paper which uses Amber ff. Can I use these  same charge values used in Amber , numerically they look pretty different than the ones in Gromos. And how is the charge group defined?

    I define one of the oxygens (O4 in the attached jpg) in the molecule as OE and the carbons bonded to it as C(C1 and C13), however there is no bond type for C(bare carbon)-OE(ether oxygen). I define the carbons in the ring having one H as CR1( CH in ring) and the rest of the carbons as C. Although it says C is a bare carbon, I think the other definitions do not fit, because it is not aliphatic, or methane or CH2. I guess the definition and nomenclature is different, is there a rule of thumb when defining the atom types? What is bare carbon and sp3 carbon with heavy atoms mean or what are gromos names of carbons that I call as C-bare carbon and CR1?

    Christian Kandt · Bonn, Germany

    Hi Ozge,

    For parameterizing molecules for the GROMOS force field I found the Automated Topology Builder run by Alan Mark's group in Brisbane a highly valuable starting point, working surprisingly well in many cases. If you feel like checking it out, here's the URL:

    http://compbio.biosci.uq.edu.au/atb/

    Hope that helps a bit. Good luck.

    Cheerz,

    Christian

  • Venkatesan Ragavendran added an answer:
    Can anyone help to run UV calculation for different solvents using Gaussian 09?

    I am trying to run UV visible calculations using Gaussian 09 programme in gas phase and also using different solvents using this keyword 

    #TD-B3LYP/6-31G(d,p) SCRF=(Solvent=Dimethylformamide)

    The calculation is not running using Gaussian 09, but it is running using Gaussian 03. Kindly suggest me if any changes in keyword. Using Gaussian 03, I have calculated for other solvents except for DMF as mentioned above. It is showing that syntax error. Kindly give me suggestions like other names for DMF for UV calculation. 

    Thank you. 

    Venkatesan Ragavendran · Sri Chandrasekharendra Saraswathi Viswa Mahavidyalaya University

    Dear Ravi kumar,,

    Thanks for your guidance. Morning I have refered the Gaussian manual and followed the same and got solution. Thanks for your efforts.

    Thank you.

  • Krishna Chaitanya Gunturu added an answer:
    How can we calculate the emission spectrum of a molecule using Gaussian?
    I want to know how we can determine the emission spectra of a molecule using Gaussian (also the keywords) and the interpretation of the result.
    Krishna Chaitanya Gunturu · University of Nova Gorica

    This error shows that the number of states given in route section (td=(nstates=6,singlet,root=1) are not sufficient enough for the convergence of the required state. Just increase the number of states and try (nstates more than 6)

  • Hassan Abdul Ghani added an answer:
    Where are the charge, sigma, epsilon parameters in GAFF?

    Hi everyone,

    I'm having trouble figuring out which columns represent the charge, sigma, and epsilon values in the commonly available Generalized Amber Force Field file gaff.dat (see attachment or search Google for "gaff.dat").

    I've come across posts in amber forums saying "it should follow the param9x.dat format". However, I am unable to pattern match my way into figuring out the gaff.dat file.

    I'm specifically interested in the charge, sigma, epsilon parameters needed for running a Lennard-Jones calculation.

    Thank you for helping me with such a mundane task.

    Hassan Abdul Ghani · University of Southern California

    Hi,

    Thank you Xiaoquan and Jason for pointing out that MOD4 contains the vdw and epsilon for each atom type. Much appreciated.

    Hassan

  • Amer Baniodeh added an answer:
    Why is the Ir(III)-S bond longer than Pt(II)-S bond?

    I notice that in the thiolate complexes of Ir(III) and Pt(II), generally, the Ir-S distances, as determined by X-ray, are slightly longer than Pt-S ones (roughly 0.1 Angstrom).

    What is the reason for that? as i always think Ir(III) should have smaller radius than Pt(II)?

    Thank you

    Amer Baniodeh · Karlsruhe Institute of Technology

    Relativistic effects. 

    This is might help. The Radius of metallic Ir is smaller . 

    http://www.technology.matthey.com/pdf/pmr-v44-i4-146-155.pdf

  • Vernon G.S. Box added an answer:
    Why does Gaussview open a whole unit cell from a CIF file while other software only visualise one molecule?

    When I open a CIF file in GaussView, I can see several molecules that form the unit cell. Opening the same CIF file in other pieces of software only visualises one molecule and draws the borders of the unit cell. On reading the file in a text editor I only see the coordinates for one molecule, so there is something that GaussView does to translate it across the unit cell.

    Any suggestions for an alternative software that could also do this whole unit cell visualisation? A collegue does not have access to GaussView, so a free option would be nice.

    Vernon G.S. Box · City College of New York

    Yes, all versions.

  • A. M. Verma added an answer:
    Does anyone here know how to generate Frank-Condon spectrum in GaussView?

    I use the 3 step approach and the error happens in the third one.The frequencies and checkpoints for the initial and final states are well generated but an error happens in the third step. 

    Sometimes generating the Frank-Condon spectrum starts and after a few lines the error happens and in most of the cases it does dot even start.

    I wonder if it happens because of a problem in entering the commands or there's a problem with checkpoints. A command sample that has properly worked is appreciated.

    Thank you in advance for your help and suggestions.

    Sara

    A. M. Verma · Indian Institute of Technology Guwahati

    Dear Sara Farahani

    did you go through with this link?

    http://faculty.ycp.edu/~jforesma/workshop/franck_condon/franck_condon.html

    this might help you...

    If you have gone through already then I would need the .com and .log files

    thanks

  • Sunwoo Kang added an answer:
    How can I run a system with total 318 electrons with g09 by MP2 method? How much will be its memory requirement?

    The system contains heavy atoms and water. Total number of basis function is 396. When the system was running with MP2, the job is running. But the water molecules were almost not moving. Energy was just fluctuating. When the number of basis function was reduced to 310 after reducing the number of heavy atoms using same basis set, waters were moving and the system became optimized. So I tried with changing the memory. But it didn't work. The first four lines of my job are

    %chk=t1.chk
    %nprocshared=16
    %mem=15GB
    # opt=modredundant mp2=SemiDirect/gen maxdisk=80GB nosymm scf=qc pseudo=read

    Sunwoo Kang · Samsung Display, South Korea

    Sorry, I fully do not understood your question but this is gonna help to solve your

    problem. But i can suggest one solution.

    If total energy is fluctuating, the scf=vshift is help to solve your problem.

    You mentioned scf=qc in route section --> This keyword gonna make your

    calculation much heavier. Please use qc keyword if you have no more chance to

    solve convergence problem. 

    Hope this help

  • Sunwoo Kang added an answer:
    Does anyone have literature suggestions on the closing of an organic molecule into a saturated 7-membered ring using DFT?

    I am struggling to complete the next step of a (in theory only) reaction pathway involving the closure of a 7-membered ring via a proton transfer to protonate a carbonyl which allows a nucleophilic attack of nitrogen onto the neighbouring carbon of the now alcohol group. The compound has not transition metals. 

    I have tried many variations in Gaussian TS searches, but I've yet to ever see the transition state and subsequent IRC pathway. Usually my TS search results in NO imaginary number, with the ring closed, and the network of proton shifts between three water molecules and the carbonly group all the way to the nitrogen being my first vibrational frequency. 

    It maybe, that the proposed mechanism just doesn't work. And that our alternative mechanism is what I should turn my attention to. However, I would like to trawl through the literature to see if anyone has shown reaction pathways of the closure of saturated seven membered rings.  

    Many thanks

    Anthony

    Sunwoo Kang · Samsung Display, South Korea

    Dear Nash

    First, sometimes, TS approach function in gaussian 09 cannot perfectly well describe TS structure. Thus, i carefully recommend you that you may find similar reaction pathway. After that, you should build geometry by your hands. I know this is really tough things to do. Sometimes, it is very useful approach way to find TS structure.  

    Second, i don't know what kind of basis set you used for TS search. Please use high level basis set with diffuse and polarization function. 

    Hope this help 

  • Binod Nepal added an answer:
    How to run Morokuma-Kitaura energy decomposition analysis in Gamess with RHF/aug-cc-pvdz basis sets?

    I want to carry out the Morokuma-Kitaura energy decomposition
    analysis on Gamess with rhf/aug-cc-pvdz level. For that I have to use keyword
    GBASIS=ACCD along with ISPHER=1. But with that I got an error saying Morokuma-Kitaura energy decomposition I cannot use ISPHER=1. Without the option ISPHER=1,

    I got an error saying: MODERN BASIS SET FAMILIES (CCN, PCN, MCP_NZP, IMCP) ARE INTENDED
    FOR USE ONLY AS SPHERICAL HARMONIC BASIS SETS. PLEASE SET ISPHER=1
    IN THE $CONTRL GROUP IN ORDER TO USE GBASIS=ACCDC .

    Would you guys please help me out for this problem? Thanks

    Binod Nepal · Utah State University

    Yes, that solved the problem. Thanks 

  • Vasileios A. Tatsis added an answer:
    How do I analyse REMD data in GROMACS?

    I am aware of the tutorial and guidelines for REMD by Mark Abraham on GROMACS website. I have 48 replicas, I calculated temperatures using the REMD temperature calculator server where the exchange probability was taken as 0.25. My replica exchange is at NPT. After 10ns of run in 12 hour, I get average exchange probability of 0.12 and 0.55 for replicas 15 and 16 respectively. Do I need to adjust the temperatures or it is ok to have such probabilities in REMD?

    My other question is about restarting REMD runs in GROMACS. I have 48 replicas hence 48 directories. Within each directory, I have multiple log files (md_0_1.log, md_0_2.log, etc) and trajectories (md_0_1.xtc, md_0_2.xtc, etc). How do I combine these files and also from other directories to obtain trajectory at particular temperature?

    Vasileios A. Tatsis · Sygnature Discovery

    Dear Neha,

    I would consider best practice, in a thermodynamical spirit, to have an overall exchange probability close to 0.25. For this purpose, you can tune: a) the differences in temperature between replicas, (and/or) b) the time between replica exchanges.

    - About your second question: Quoting from Gromacs documentation (http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B)

     "There are some times you want a trajectory that has continuous coordinates, despite the "jumps" in ensemble space. This means chopping up each trajectory file into pieces and pasting them back together in the right order. The Perl script demux.pl installed with GROMACS will analyse a single REMD .log file and writes two special .xvg files that describe the transformation matrices for the trajectory time series from one form to the other, and back. trjcat -demux can use these files to do the cut-and-paste on the trajectory files for you." 

    Happy REMD simulations! (May the replica be with you)

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