Questions related to Atoms
Hi. I am working on a project with VASP with MoO3 lattice and recently I found out that I have to consider spin polarization in my calculations. So, now I do not know what value I should consider for the MAGMOM of Mo and O atoms in my INCAR file, can anyone help me in this regard?
#VASP #MAGMOM #SPIN
I have a structure of nanoonion which is basically fullerene units with different number of carbon atoms structured like the onion (possessing common centre). So there are no repetitive cell unit. Can I optimize the structure using Quantum Espresso? In a broader way, can I optimize any structure which does not possess any repetitive unit using Quantum Espresso?
What is the energy of a substance due to the movement of its molecules or atoms and energy is the sum of energy in motion and stored energy in objects?
I would like to replace the Zn atom on the surface of ZIF-8 particle by the ion exchange.
I have the XRD and TEM data of ZIF-8, how many Zn atoms on the surface of this particle?
and how many kpoints should we select for a 2x2x2 supercell having 52 atoms for phonopy calculations?
I would appreciate it if someone could help me with the following question.
Instead of calculationg the angle between three atoms , I'd like to calculate an angle between the center of geometry of each of three groups of atoms, I've looked at the options gmx angle and I didn't find one like in gmx distance -select.
Any help is appreciated.
I docked the inhibitor to the metalloenzyme and the next step was the minimization of the complex. Unfortunately, during the minimization protocol, I got the error as below:
>Solvent file: XXX\bin\Windows-x64\..\..\data\water.slv
>Block specifies desired NFIELD -- accepting block
>RDSOLV: missing params for atom number 36261 (type n2) in .slv file, solvation model 3
>MINI: Error generating interactions
>Problem in minimization of distinct structures.
>Skipping input structure due to forcefield interaction errors.
>BatchMin: normal termination
The atom number 36261 is the Nickel 2+ ion. I've tried to change for the one without charge, but still the OPLSe do not operate with it.
My question is about: how to add the nickel ions to the FF with proper parameters.
I am trying to dock a Ruthenium complex with a protein. As expected, Vina does not recognize Ru atom type and throws the following error:
"PDBQT parsing error: Atom type Ru is not a valid AutoDock type (atom types are case-sensitive).
> ATOM 3 RU UNL 1 0.177 1.341 0.016 0.00 0.00 +0.000 Ru"
I have tried to modify the parameters by adding the Ru parameters (with case-sensitive alternatives), however the error persists.
Please help me to rectify this error. I am not able to find any documentation on the same for Vina. I am performing the calculations on a LINUX OS.
It's a dumb question maybe, but I'm not sure how to proceed.
Suppose you have two different models which generate molecules (in the form of coordinates of atoms). The molecules generated by models are not the same.
Next, you have a method to evaluate energy of a molecule (given atomic coordinates, it outputs a number). I can also optimize atomic coordinates with this method.
The question is, how to compare these two generative models in terms of energy?
My guess is that I can run minimization for each configuration and can evaluate dE = E_final - E_initial. But how can I compare/aggregate dE between different molecules? My guess is that to have a crude estimate one can divide these quantities by the total charge of the nuclei in the molecule (which equals to the number of electrons for neutral molecules). Is this reasonable or better ways exist?
I'm simulating on Quantum Espresso the H adsorption on Ni(OH)2 surface. However, upon relaxation of the system, H binds with one of the O atoms of the surface and forms water, which is not an expected result. Is there any specific procedure to simulate adsorption that I am not taking in account?
I am writing to seek assistance on a matter related to n2t file generation. I am using GROMACS and charmm36 force field in my work. I am covalently attaching a short polymer(poly-peptide) to a nanosheet with the carbonyl carbon of the polymer attached to the nitrogen of the nanosheet I obtained the parameter(itp file) for the polypeptide from CGENFF then added the corresponding atom types and charges from the itp to my n2t file the monomer of the poly-peptide is histidine and it’s itp file has various hydrogen atom type along with carbon types with different charges I have added them all in the n2t file in the same sequence as in the itp since most these atom types are attached to carbon when topology is created using x2top wrong type of carbon and consequently wrong charge is assigned to the atom of my structure. I want you to note the hydrogen types as well as the nitrogen type NG2R51 in the topology file at line 134 it is supposed to be a NG2S1 nitrogen type with a -0.555 charge. There are many other atoms whose atom type was supposed to be different. How can I obtain correct topology.I am attaching the itp file(plh.itp) along with the ss of topology and n2t file. Any guidance or pointers would be of immense help. Thank you for your time.
I am not a specialist in physics or chemistry, which are essentially the field of science that studies the composition and behavior of matter, and its main component widely known is the Atom. I am reading a Spanish book called "RESPUESTAS SORPRENDENTES A PREGUNTAS COTIDIANAS" by Jordi Pereyra, a Spanish science communicator and mechanic engineer. The book is a systematic order of answers to questions that children usually have, for example; "Where do Helium balloons go?", and stuff like that. So, I've been reading the first chapters, and it's mostly all about Atoms, and by the definitions that I know about Biology, mostly from Wikipedia, Atoms seem to be pretty much alive, maybe even more alive than humans.
My uninformed-citizen definition of life is that matter can be distinguished from other matter that has the following qualities; growth, metabolisms, reaction to stimuli, reproduction, interaction, and self-sustaining.
So, humans does have those qualities, but I can argue that Atoms also have.
- GROWTH; An Atom can growth in volume, density, and in particles, through processes that the Atom does not choose, just has Humans. (Humans in early stages of life does not chooses to growth). The Atom can decrese and increase its volume by radiation. The Atom can radiate, or be a victim of radiation, and become a bigger and heavier atom through Alpha Particles.
- METABOLISMS; Atoms, in order to mantain a stable structure, and have a longer life, (which can be compared to the semi-voluntary process of survival in humans and animals), they usually (only in case they are unstable) radiate an Alpha particle or a Beta particle, in order to mantain its structure.
- REACTION TO STIMULI; An example of RTS; Grab a spoon of a neutron star, and then teleport that spoon with a Neutron Star material into the surface of the Earth, the Atoms (or Protons and Neutrons) will go crazy due to the stimuli of preasure.
- REPRODUCTION; By radiation, and Atom can create other Atoms in form of Alpha Particles, which are identical to Helium-4.
- INTERACTION; Atoms between each other can create molecules, which are groups of 2 or more atoms. These molecules has different characteristics from each other, for example, Dihydrogen Monoxide is one of the basis of life here on earth, but Ozone, has other characteristics, which are harmful for animals here on earth, but good to prevent solar and cosmic stuff entering the Earth. This can be compared to human social groups, even animal interpersonal groups. This due to the characteristics of the behavior of each persons that is member of an official or unofficial (unprofessional) group. That group can be good at something, but bad in another, just as molecules.
- SELF-SUSTAINING; Atoms always will try to reach stability, by radiation, and they will eventually be willing to turn into another element in order to mantain its life.
So, these qualities that make life possible, are also applied into Atoms. So that's what I was thinking when I was reading the book mentioned. What ResearchGate members, specialists or non-specialists on physics, chemestry, or biology think?
Which of the properties of atoms is the most suitable reference for the kind of bond that will take place between among them?
I would like to dope ZnO with Fe and found that
to Create a super cell of ZnO with a desired concentration of Fe atoms say 10%.
I have Replace the Zn atoms with Fe atom in the supercell.
My question is how many atoms of Zinc I need to replace with Fe to get the following structure Z(1-x)FexO say (x= 10%) or other
I was trying to optimize a compound with 165 atoms using the DFT method. The GEN basis set and B3LYP functional were used there. But I am getting the Error termination in NtrErr: NtrErr called from FIOCnC. I rebuilt the input structure and went through the same calculation, and I got the same error again.
Kindly help to solve it.
I have been running a job by VASP. My structure is a cluster(46 atoms) + one metal. when i want to optimize it, at the middle of the run, i saw this message: please rerun with smaller EDIFF, or copy CONTCAR
to POSCAR and continue ....and it doesn't converge...
my INCAR file is:
PREC = Normal
EDIFF = 1e-5
ENCUT = 400
NSW = 3000
!ISPIN = 2
IBRION = 2
ISMEAR = 0 ; SIGMA = 0.0050
IVDW = 11
LORBIT = 11
NELM = 120
I am looking to understand geometry of metal center in a coordination compound. Shape is one such programme to find the exact coordination environment around the central atom. anyone has any idea on how to use it?
I am doing VASP calculations with a bulk triclinic lattice system involving transition metals Cr and V. I know that you can check the spin for the entire system with the OSZICAR file from VASP but is there a way to check the spin multiplicity on each individual V atom and each individual Cr atom in the system to see how many unpaired spins each transition metal atom has?
I'm trying to optimize methyl iodide, and I wanted to use Aug-cc-pVTZ-PP as the basis set. what is the keyword for this basis set? (I'm very new to theoretical calculation and I'm trying to learn on my own)
Hi all, Anyone can help me to fix the problem, VERY BAD NEWS! internal error in subroutine IBZKPT:
Reciprocal lattice and k-lattice belong to different class of lattices. Often results are still useful... 96
VERY BAD NEWS! internal error in subroutine IBZKPT:
Reciprocal lattice and k-lattice belong to different class of lattices. Often results are still useful... 96
I try it many times and I have same structure but with different atom such as Ca and it is work and finish however I used same sitting ??
I attached the files bellow related to this problem:
I am conducting a protein-metal docking in Autodock using an Arsenic compound and am unable to produce a proper GLG file. When I complete the autogrid I get the following error in the GLG file:
GPF> parameter_file AD4.1_bound.dat
Using read_parameter_library() to try to open and read "AD4.1_bound.dat".
/autogrid4.exe: FATAL ERROR: Sorry, I can't find or open AD4.1_bound.dat
/autogrid4.exe: Unsuccessful Completion.
I am unsure if the problem comes from an issue with the software, parameter file, or even python? The python shell shows some errors, but I don't know if that is just because the parameterization was unsuccessful.
To solve the issue I have tried the following steps but they did not fix the error:
- After setting up grid, Output>Save GPF>”File.gpf”. Then opening up the File.gpf in the folder and adding “parameter_file AD4.1_bound.dat” to the very first line.
- After saving the grid, selecting Other Options>Parameter Library Filename>Select file>Edit Parameter Library>Select File>OK>Output>Save GPF>”File.gpf” to directly add the parameter file to the GPF file using Autodock
- Copying the parameter files from the vina website and adding only additional atoms of interest
- No spaces in files/pathways and ensuring everything in the same workspace folder
- Unchecked Read-only from properties of folder
- Ran Autodock Tools as an administrator
- Set "Startup Directory" as "C:\Workspace" from AutoDock Tools preferences.
Thank you very much.
Dear research gate community,
I am trying to simulate a boron nitride nanosheet covalently functionalized with a short chain polymer using charmm36 force field in gromacs. I obtained the str file of polymer from cgenff and obtained its prm and itp file. Later I prepared a n2t file for the system including the nanosheet atoms and polymer atoms( the atom types were defined as per the atom types in itp file ).I was able to generate the topology file but I am doubtful about my approach as I only used atom types and charges and not the whole itp all the parameter like bond angles, dihedrals were automatically generated. It would be great if someone could guide me whether the approach is correct or not and how can i incoporate the itp parameter for the polymer. Any guidance would be of great value. Thank you!
#charmm36 #GROMACS #CGENFF
In the process of doping in semiconductors:
1: How can a dopant atom take the place of a host atom in a crystal lattice? In fact, with what power can the dopant atom prevent the host atom from forming a bond with its other counterparts and establish a bond instead?
2: After the site of a host atom is occupied by a dopant, what happens to that host atom whose site is now occupied? In fact, where and in what new form does the fired host atom fit or establish a new bond? Should this driven host atom also take the place of another host atom? And is this process repeated sequentially? What then happens to the last ejected host atom?
For the calculation of the total energy in VASP, it is recommended to use tetrahedron method with Blöchl corrections (ISMEAR=-5). And for 2D slabs in the z direction (perpendicular to the surface), it is recommended to give only 1 k point since there is vacuum above surface (The middle layers we freeze the atoms).
But when ISMEAR=-5 is used in VASP, an error comes
Tetrahedron method fails for NKPT<4. NKPT = 3
So should we use Methfessel paxton/Gaussian smearing in this case?
Can anyone please answer, how to dock the palladium complex with protein using Auto dock vina 1.5.7 software. It was showing below error while docking palladium related complexes. How to resolve this?
" Parse error on line 6 in file "C4.pdbqt": ATOM syntax incorrect: "Pd" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive."
I am reaching out to seek guidance and assistance regarding a challenge I've encountered while attempting to simulate boron nitride nanosheets using the CHARMM force field, specifically CHARMM36. I have followed a tutorial (http://chembytes.wikidot.com/grocnt#toc) that successfully guided me through simulating graphene; however, when attempting the same process for boron nitride, I encountered an error that stated: "CANNOT FIND FORCE FIELD FOR X ATOMS WITH X BONDS."
>I have attempted various approaches to overcome this issue, and I would like to outline the steps I have taken so far:
>I generated the initial boron nitride nanosheet structures using GaussView and saved them in PDB format.
>I used VMD (Visual Molecular Dynamics) to convert the PDB-formatted structures into GRO format, following the procedure outlined in the tutorial.
>I attempted to use the editconf tool to prepare the simulation box and system for further processing.
>I defined a .n2t file to specify atom types for boron and nitrogen atoms.
>I extended the .atp file to incorporate the newly defined atom types.
>I updated the bonded and nonbonded parameter files (.itp) to include relevant parameters for boron nitride atoms.(I obtained the parameters from literature but it would be great help if someone could also recommend the force constants that could be used.I am attaching the n2t file along with the gro files.
If anyone has successfully simulated boron nitride nanosheet or has expertise in this area, I would greatly appreciate your guidance and insights. Specifically, I am looking for a reliable method to simulate boron nitride nanosheets.
#boronnitride #MD simulation #CHARMM #GROMACS
Hellow Everyone .
I have a query that i have build a monomer of both phospholipids and glycolipids for Md Simulation but the problem which i face is that once i go to tool/software and put the molecules click on label atom than their numbering come on randomly can't come on proper manner than how to solve this issue thanks in advance
Are we trying to find the source of life by zoom into atoms and zoom out to see the universe?
Is that really the correct question to answer?
Don't we see by this subject we can't understand the reason of living?
After seeing nothing but glumy objects by zooming in and seeing repetitive star born and death pattern by zooming out, what we will reach except telling people the universe is created from nothing?!!!
Or we turn around and look for a more acceptable and better question?
Who can find a better question which answers and finds a better puzzle piece?
I want to take Hirshfeld surface for two components of disorder for my complex. Can I use Olex2 to get component1 cif by deleting the disordered atoms from parent compound in Olex2 and save it without further refinement because the refinement of componet1 gives the disordered parent complex. Then I would use the cif to get the Hirshfeld.
Thank you and best regards
Adnan M. Qadir
Could anybody explain me the meaning of the data point “number of atoms” that is shown for any material on the material project website? I thought that it was supossed to tell the number of atoms per unit cell, but, in many cases, it doesn’t make any sense to me. For instance, TaC (https://next-gen.materialsproject.org/materials/mp-1086: (Cubic, Fm-3m, 225)) exihibits a fcc crystal structure and, thus, should feature 4 atoms per unit cell. However, “number of atoms” on the website says that it’s 8.
What am I missing?
I am trying to run a calculation using the HF/LANL2DZ level of theory, and am interested in visualizing the canonical orbitals and the basis functions. The molecule of interest is pentagonal planar (D5h point group), and I would like to choose the coordinate system such that the py basis functions on the terminal atoms are pointing towards the center of the molecule.
Does g09 support this? What keywords would I have to add to the route section to achieve this?
Thank you very much!
Hi there! I'm a physics engineering student student working on a materials science project, and I'm currently running a simulation using LAMMPS. However, I've encountered an issue with the error message "ERROR: Lost atoms: original 182322 current 181371 (../thermo.cpp:438) Last command: run 10000" when running the script. My goal is to simulate the collision of a Cu nanoparticle with a Ni surface under normal conditions. I have attached the input file for reference.
The problem seems to be related to the "velocity nickel create 100.0 12345 dist gaussian" command line. When I include this line in the script, the program gives me the error. However, if I remove that line, the code works perfectly, but I lost information.
I want to resolve this issue to make the simulation more realistic.
Could you please help me with this? I'm eager to improve the accuracy of the simulation. Thank you!
I'm attepting to do NICS analysis on a reaction intermediate, but currently the molecule is oriented in a random way and the aromatic ring I want to analyse is not in the XY plane. Does anyone know how to reorient the coordinates of a molecule in gaussview without changing their relative positions? Currently the only way I've thought of is manually changing the cartesian coordinated but am hoping there's a method that won't require hours of labourious manual atom movements
Here the Ni has equilibrium lattice constant of 3.52 and I applied the 20% strain on x y and z axis.
calculation = 'scf'
verbosity = 'high'
tstress = .true.
tprnfor = .true.
prefix = 'myprefix'
pseudo_dir = '/home/ashwani/PP/PBE_ONCV'
ecutwfc = 50
ecutrho = 400
occupations = 'smearing'
degauss = 0.001
smearing = 'mp'
nspin = 1
ntyp = 1
nat = 4
ibrav = 0
electron_maxstep = 200
mixing_mode = 'plain'
mixing_beta = 0.7
diagonalization = 'david'
Ni 58.6934 Ni.UPF
6 6 6 0 0 0
3.72000000000000 0.00000000000000 0.00000000000000
0.00000000000000 3.72000000000000 0.00000000000000
0.00000000000000 0.00000000000000 3.72000000000000
Ni 0.0000000000 0.0000000000 0.0000000000
Ni 0.0000000000 0.4731182796 0.4731182796
Ni 0.4731182796 0.0000000000 0.4731182796
Ni 0.4731182796 0.4731182796 0.0000000000
Hi, I have a list of output files after a Gaussian calculation, and I want to get the charges of carbon and nitrogen atoms in the constant skeleton of these molecules to use them later as QSAR descriptors. How can I do it automatically?
Let's say I have an XRD pattern for BiFeO3 doped with 5 at-% Ti occupying the B-site (nominally BiFe0.95Ti0.05O3). I start with a BiFeO3 CIF file and add the Ti on the Fe site (same position with a frac of 0.05). Should I refine the positions of the atoms later on?
Are there any other things to keep in mind when adding dopants like this?
I used NWChem to calculate hyperfine coupling constant as follows:
Total Spin Density (Fermi Contact Term)
Atom x y z Density (a.u.) Aiso(MHz) Aiso(Gauss)
1 14-N -5.40277 -2.13248 9.71067 -0.000101 -0.032739 -0.011682
The output section contains above information and later on it shows anisotropic interaction as follow:
Anisotropic Interaction (Spin-Dipolar Term)
Atom x y z
1 14-N -5.40277 -2.13248 9.71067
Spin-Dipolar term (a.u.)
xx yy zz xy xz yz
-0.000423 -0.000610 0.001033 0.000422 -0.001299 -0.000812
Principal Comp. of -hf- tensor (au) Anisotropic -hfcc- (MHz) Anisotropic -hfcc- (Gauss)
-0.001192 -0.000911 0.002102 -0.045957 -0.035118 0.081075 -0.016399 -0.012531 0.028930
Orientation of the principal axis of Hyperfine Tensor w.r.t absolute (molecular) frame
0.828572 -0.296088 -0.475185
0.151180 0.935514 -0.319309
0.539086 0.192732 0.819903
Can anyone have idea about these results?
I have tried to contact the BIOVIA DiscoveryStudio support team, somehow my browser does not allow me to open their "contact form". I am trying to visualize and perform an analysis on a protein:smaller molecule complex. The smaller molecule happens to be a long peptide. Whatever I do with the PDB (change ATOM cards to HETATM, change residue names to PEP, UNK, LGD, introduce MODEL and ENDMDL cards) DiscoveryStudio indicates the input PDB file doesn't contain any ligand. Would any on ResearchGate have an idea of how to specify that a part of a coordinate file is the ligand, so that DiscoveryStudio 2021 recognises it as such and allows me to proceed? Thanks, Fred.
Regarding the importance of using Metals (single atom, nanoclusters) as an active sites on a support (Metal Oxides, Metal sulfides, etc.) for enhancing the photocatalytic chemical reaction (H2 evolution / Water splitting/ CO2 reduction), which active sites will be good ; Metal single atom or Metal Nanoclusters or Mixture of them?
I want to calculate the HOMO-LUMO coefficient for each atom of my molecules. I am using Gaussian software for calculations. As I can see in multiwfn manual, I can get the orbital percentage but not getting the HOMO-LUMO coefficient. Herein, I have attached an image of a reported molecule depicting the HOMO and LUMO coefficient for each atom. Please help me regarding this.
Literature reference: https://doi.org/10.1007/s00706-020-02653-y.
I downloaded my pdb file from RCSB. Cuz I want to use amber tleap, I used pdb4amber to convert the PDB file. Then the error occurred:
GLU_29 misses 4 heavy atom(s)
ARG_102 misses 6 heavy atom(s)
GLU_242 misses 4 heavy atom(s)
ARG_243 misses 6 heavy atom(s)
I then checked my pdb file downloaded from RCSB. These residues do miss some heavy atoms. What should I do then to add the missed atoms. I know what atoms missed, but just do not know how to add them.
Hope I could get your help! Thank you very much!
Hi, guys. I started doing some dockings a few days ago and there was an constantly error showing up on the autodocktools cmd:
"swig/python detected a memory leak of type 'BHtree *', no destructor found." (PFA a printscreen of the error).
The error kept showing up after every command i gave. For example, after every missing atom added it showed up again. I didn't mind at first, because everything was working just fine, even though I was wondering if my results would be realiable with such an error.
But now, there is another error showing up on the autodock (You can also find a printscreen attached), and i can't dock anything anymore. I have already tried reinstalling autodock and MGLtools.
Has anyone had this same errors? Would you know how can I solve it? Just making clear that I'm not familiar with programming.
Thank you so much!
I am currently working on the simulation study of a complex whose ligand cannot be automatically parameterized. I have been using AMBER to do the parameterization, and now I have obtained the .lib for the ligand. I want to load the parameter to the complex to prepare the input file for simulation. After changing the residue and chain name of the ligand in the complex PDB, I did:
tleap -f oldff/leaprc.ff99SB
>complex = loadpdb deoxyCom.pdb
and it added missing heavy atoms that are not included in the parameter lib. (the whole message is as tleap.txt)
how should I deal with the problem and prepare the input file for MD?
I am trying to find out the logic in not identification of hydrogen bond interaction in the charged NH+ from the ligand part with the Asp residue from the protein. That incidence has been observed in both crystal structure and docking results since these two atoms resides closely (~2.4 angstrom). They are forming salt bridge interaction rather not forming Hydrogen bond.
I would like to know what is the reason behind this interaction.
Thank you in advance.
I am new to amber any trying to use xleap to make a tetrapeptide tuftsin. After solvation with TIP3PBox 14.0 iso, when I try to save the inpcrd and prmtop file using command
saveamberparm foo tuftsin.inpcrd tuftsin.prmtop
it gives following message
WARNING: There is a bond of 3.610664 angstroms between:
------- .R<WAT 886>.A<H1 2> and .R<WAT 886>.A<O 1>
WARNING: There is a bond of 4.162462 angstroms between:
------- .R<WAT 886>.A<H2 3> and .R<WAT 886>.A<H1 2>
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
-- ignoring the warnings.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 11 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
I am not getting how to solve this error message.
I am trying to optimize a 48 atom heterostructure using wB97XD hybrid and 6-311G++(d,p) basis set in Gaussian 16. It's been more than 24 hours and the output file is saying 'no special action if energy rises' only. What should I do? Kill the process? Or wait? Number of processors are 10 in the workstation.
I'am using QE for surface study, however to preserve calculation timing and RAM usage, I need to fixed/freeze the atoms constituted by the central layer. For example, I cut FCC Co2FeSi along the lattice direction 001 with 13 layers and 15 angstrom as a vacuum. I am confused or don't know to freeze the central 3 layers using QE.
I will be grateful if anyone can help me in this query.
Thanks in Advance.
I was giving first command of gromacs, I selected groos forcefield no. 14 the united atom charge but after that I encountered the error while funning the command pdb2gx that "Atom HN1 in residue PRO 4 was not found in rtp entry PRO with 9 atoms while sorting atoms." So how to correct it plz let me know. I am attaching the file below which contains chain A and 2 ligands,
Thanks and regards
Eg. How to calculate radial probability density fpr Zn and Cd atoms. Please ?
I am working on a molecular dynamics simulation in protein-ligand system, using NAMD software, and I got the following error.
"FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HGA1 CG3C51 SG311 (ATOMS 1753 1752 1770)"
The atoms mentioned above belong to the ligand structure. The .str and topology files for the ligand were generated using Charmm-gui. Can someone help me to solve this failure? Thank you in advance.
I am doing molecular Dynamic simulation using GROMACS software. Currently i am working on the sugar modified double stranded DNA, for which i need to generate a force field. I tried CHARMM General Force Field, but i guess its applicable only for small molecule. I also tried GAFF where I tried generating Force field for the nucleotides(with modified sugar) by patching them with NMe/ACE. But the calculated charge on the patched group is not zero and overall charge of the nucleotide is not integer. My system has around 2000 atoms. Please suggest how I should proceed.
I am currently screening more than 2000 compounds virtually on Vina, but I would like to perform covalent docking. Unfortunately, Vina's functionality is limited as its requires manual designation of the reactive atoms on the ligands. Is there any alternative that is free for academic purposes and suited for this sort of task?
I'm working with a system of 192 atoms. I've already relaxed the structure (with ISIF=2 and ISMEAR=0) and achieved the required accuracy. Then, as per the instructions in the VASP manual, I ran the SCF calculation. After that, I copied the obtained CHGCAR file to the DOS directory and attempted to run the calculation. However, every time I receive the following error message:
"WARNING: The chargedensity file is incomplete. ERROR: The charge density could not be read from the CHGCAR file for ICHARG>10."
I have double-checked that the file is copied to the correct directory, and it is complete (I can see the augmentation occupancies for all 192 atoms. Additionally, I have verified the dimensions (NGX, NGY, NGZ, NGXF, NGYF, and NGZF) in the CHGCAR file, and they are all accurate. Can you please assist me with this issue? The INCAR file is given below.
ISTART = 1 ISPIN = 2 ICHARG = 11 LREAL = A ENCUT = 520 PREC = Normal ISMEAR = -5 NELM = 60 NELMIN = 5 EDIFF = 1.0E-05 LORBIT = 11 NEDOS = 1000 NSW = 0 IBRION = -1 POTIM = 0.5
Recently, I have proposed a theory about Black Holes:
Black hole basically stretches any object headed right into the singularity of the Black Hole, making it smaller and smaller (Spaghettification). So once the object reaches at the size, reaching a Quantum Level Size (smaller than an atom), the gravity of the black hole will get flipped and will work in the Reverse Direction; gravity at the quantum level is “repulsive” instead of being attractive. So due to this “repulsive” gravity, this Black Hole will throw out that object, it maybe in the form of Hawking Radiations, or the Black Hole will be in a Superposition State, Black and White Hole simultaneously, and will work as a white hole, and this “superposition” state of the Black Hole would be Wormhole.
That means, a Black Hole is existing as a White Hole simultaneously, it is just that an object has to be infinitely small to escape a Black Hole.
I am performing TDDFT emission spectrum calculation for the first time. I have used below mentioned route section command
# opt td=(singlets,nstates=10,root=1) b3lyp/gen pop=full geom=connectivity
My molecule have C, H, N O for which I am using 6-31G** and Ge for which I am using LANL2DZ. The molecule comprised of 74 atoms in which one atom is Ge rest 36 are carbon and nitrogen, others hydrogen.
Can anyone please tell me am I going in a right direction or not.
Also, can anyone comment on the time it usually takes to complete the run.
Thanks in advance for the help.
We assume that N. Bohr knew brilliantly that his previous description of the spectrum of the hydrogen atom via a single principal energy quantum number was insufficient to describe the fine structure of the hydrogen atom and so he introduced the interpretation of Schrodnger's equation to generate 4 quantum numbers n, l, m, s (primary, azimuthal, magnetic and spin quantum numbers) for a more complete description of the H2 atom.
However, this interpretation requires an instantaneous entanglement of subatomic quantum particles through space.
A. Eistien admitted the probabilistic nature of SE but only objected to instantaneous entanglement because it would violate the principles of the special theory of relativity.
He called the latter a frightening action from a distance.
The question arises: can we succeed in integrating the two points of view?
I use crsytal explorer, my cif file open than ı choose all atoms but the energy calculation button is not active, what can I do?
I am studying about the Stark effect. I have read about some calculations with using the pertubation theory for state n=2 of hydrogen atom. In here, the energy of this level are lifted up and lifted down by 3ea_0 E (a_0 is Bohr radius; E=electronic field). How about with state n=3 or higher state when the atom is applied by a static electronic field?
Hi, What is the crystal structure of a Titanium-Tungsten film? Titanium by itself is hexagonal close-packed (HCP) while Tungsten is body-centered cubic (BCC).
my other question, why is TiW is a better barrier while Ti is not? does this have to do with the packing/density of the atoms?