All Questions
Tagged with intermolecular-forces computational-chemistry
28 questions
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301
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Physical origin of induction and dispersion energies
I am reading this book on non-covalent interactions. Chapter 1 states that there are 3 types of non-covalent interactions:
Electrostatic interactions, which are just the coulomb interactions between ...
2
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0
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64
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How to model a molecule of benzene surrounded by 100 molecules of water with molecular dynamics?
I have experience calculating molecular properties (mostly DFT). However, I would like to spend some time on molecular dynamics methods. I would like to ask your advice to direct me towards a program ...
user55257
3
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0
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175
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What are the cheapest basis sets able to model intermolecular dipole interactions inside a metal complex and give good relative energies, with DFT?
As a example, If I have a square planar complex of a cation with both a weakly polar ligand (X) and strongly polar ones, like ammonia and water I expect a bit of stabilization due to formation of a ...
- 663
2
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117
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Is Tkatchenko's MBD-NL method self-consistent?
I have a question regarding Tkatchenko's [1] new nonlocal many-body dispersion method (MBD-NL). Does anyone know if it's a self-consistent method? I read this paper many times but I'm still not sure.
...
- 29
8
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1
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How to obtain curve energy and non-bonded interaction parameters (e.g. Lennard Jones parameters) with Gaussian?
I am parameterizing a force field and would need to obtain non-bonded interaction parameters of atoms (e.g., Lennard-Jones parameters).
My primary idea is to obtain a potential energy curve using the ...
- 321
12
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3
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1k
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Why aren't the Anton computers used more widely?
The Anton computers are purpose-built by DE Shaw research for molecular dynamics simulations. They achieve performance up to an order of magnitude faster than can be achieved with commodity hardware, ...
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1
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0
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84
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Is the 12-6 Lennard Jones potential a good description of van der Waals interaction energy?
It seems to me that the Lennard Jones potential oversimplifies the more complex nature of van der Waals forces. However, in most of the MD simulation package, this is generally accepted.
- 329
2
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1
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Radial pair distribution function (VMD). How to define it for a water NaCl system with multiple Na and Cl?
I'm struggling to understand a paper in which someone has presented radial distribution functions (RDFs) for a system that contains multiple Na, Cl, and water atoms/molecules. I don't know exactly ...
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7
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1
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How to calculate Lennard-Jones potential with quantum mechanical methods
I want to know the procedure to calculate the Lennard-Jones potential for a metal-halogen pair (specifically vanadium-chlorine). Is it possible to calculate using any QM packages like Mopac, NWChem, ...
- 517
1
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1
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473
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Lennard-jones cut-off
I am using a Lennard-Jones potential in a computer simulation and I was wondering if i should place a cut-off for low distances since the potential blows up quickly making the calculations quite ...
- 73
1
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1
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519
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Difference between Force Field and topology, and other related questions
I am performing some Molecular Dynamics computer simulations and I am learning about the various Force Fields (FF) such as OPLS-AA, OPLS-UA, AMBER, etc.
Many things are still unclear to me. I put ...
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6
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2
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229
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Force Fields and units
I am a math student trying to implement a simple force field in python for determining the energy of a small molecule and trying to minimize it in order to find a stable configuration. I was wondering ...
- 73
10
votes
1
answer
663
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How DFT-D3 incorporates coordination number (CN) into C6
I'm reading Grimme's DFT-D3 paper
but really puzzled by how the $\mathrm{CN}$ is considered in the calculation of $C_\mathrm{6}$ coefficients. (Stefan Grimme, Jens Antony, Stephan Ehrlich, and Helge ...
- 977
2
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1
answer
223
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Recommendations for electrostatic potential surfaces
Are there standards for density cutoffs, colours and colour mappings for electrostatic potential surfaces?
I observe that people use many different values.
For instance, this article (in Fig. 1a) ...
- 2,883
10
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112
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Which potentials are suitable for molecular dynamics simulation of simple explicit solvents?
Which potentials (force fields) are suitable for adequately simulating (mixtures of) explicit solvents? Interesting rheological properties include viscosity, surface tension, heat capacity.
- 4,285
7
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1
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229
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Computational Chemistry: calculation of sterical effects
Is there a way to calculate sterical forces between atoms/groups of atoms (preferably with free and open source tools)? I have heard that this is possible within the framework of NBO. I am using ORCA, ...
- 2,804
3
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1
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296
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Ordinary differential equation for molecule collision
I have no background in chemistry.
But, I have a good background in mathematics and computer programming.
I have planned to simulate the collision of two simple molecules $\ce{Br2}$ and $\ce{H2}$ ...
- 133
9
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1
answer
2k
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How to save the force on a molecule in GROMACS?
I am a new student of molecular dynamics. I have started using GROMACS a month ago.
I have a small box of 8192 molecules each with 3 atoms. I froze the last molecule and ran the simulation. I even ...
- 91
6
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1
answer
533
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Formulas for non-bonded interaction energies
If one were to calculate the non-bonded interaction energy between two atoms, this would equate to the sum of the vdW + electrostatic potential energies:
$$
E_{\text{non-bond}} = E_{\text{vdW}} + E_{\...
- 63
8
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2
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9k
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Significance of single point energy when calculating interaction energies
I am currently investigating about the interaction behavior of a few atoms in certain conditions.
Is it possible to use the concept of single point energy to represent the atomic interaction energies ...
- 683
11
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1
answer
2k
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How to read TINKER's force field parameters
I'm going to parameterize AMBER force field for the simulation of some small molecules. I have found the parameter sets provided by TINKER at here.
I'm stuck here because I couldn't find any ...
- 113
4
votes
1
answer
115
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Charge consistency in fragment qm/mm methods
I'm calculating the multipole moments on several fragments of a molecule. What are some procedures to ensure that the charges etc are representative of the complete molecule? How do I ensure I'm not ...
- 41
3
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1
answer
191
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How to get a protein's dihedral angles ordered by variance?
The setting: I want to simulate protein docking and let some dihedral angles vary, but in order to keep it low-dimensional I have to select those which are most likely to change.
What I've thought of ...
- 205
7
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1
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2k
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Why are C6 dispersion forces named C6?
I'm reading about water models and their dispersion coefficients, and going back to S. C. Wang's work according to the citation of an equation (Google books here)
As you can see one citation's to a ...
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6
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2
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131
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What's the reason for discrepancy between DFT calculated image and NC-AFM-acquired one in this article?
Looking at the images in this article, I've noticed that the molecule electron density images showed as calculated via DFT look very symmetric, while those obtained by NC-AFM appear somewhat distorted....
- 1,005
2
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0
answers
1k
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Structure of fluoroalkylsilane
I want to use FAS (fluoroalkylsilane) in my molecular dynamics study. How can I find it's real structure? So that I can find proper forcefield for simulating the molecule. It would be very nice if you ...
- 141
36
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1
answer
6k
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Natural Bond Orbital analysis: Significance of stabilization energy determined by 2nd order perturbation
PREFACE: I am no expert on this topic. My questions at the bottom may be off base. I have some experience with symmetry-adapted perturbation theory (SAPT) when it comes to analyzing intermolecular ...
- 4,637
2
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1
answer
182
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Coarse-grained force field for ion–water interactions
I want to simulate, at a very coarse grained level, the interaction of water molecules with metal ions, specifically Calcium and Potassium. Is there a standard force field for this. I was told to use ...
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