All Questions
Tagged with molecular-dynamics computational-chemistry
46 questions
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How to derive missing parameters for modified nucleosides (OL15/OL21)
I am new to molecular dynamics and am currently working on modified DNA/RNA nucleosides, derived from the OL21 and OL15 available templates, respectively. I would like to stick with these force fields ...
- 149
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33
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Functional form of dihedral energy term in molecular mechanics: why always cosine?
As far as I can tell from looking into the most popular reference texts, it seems that the dihedral energy term in a molecular mechanics forcefield always uses cosine function (more specifically a ...
- 63
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34
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Why Car Parrinello Molecular Dynamics doesn't need an SCF calculation at every time-step?
Reading the various terms of the Lagrangian in CP-MD I'm trying to understand why there is not an SCF procedure hidden there.
In fact, it seems to me like the second term of the Eulero-Lagrange ...
- 177
3
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1
answer
129
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How to embed multiple molecules with rdkit?
I am new to rdkit and struggle with something I thought would be simple: I want to randomly embed two molecules in 3D space so that the two do not overlap. This is to generate an initial state for ...
- 133
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25
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When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?
Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
1
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105
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The need for accurcy in constrained molecular dynamics simulations
In constrained molecular dynamics a system of differential algebraic equations
$$\begin{align} \dot{q} &= v, \\ M\dot{v} & = f(q) - G(q)^T \lambda, \\ g(q) &= 0 \end{align} $$
is solved. ...
- 111
3
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2
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179
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Why does a symmetric stretch mode not have an imaginary frequency?
Currently studying potential energy systems and our professor asked a question at the end of a lecture and I can't wrap my head around it.
He said, "Picture a 2D PES for the simple reaction of H+...
- 137
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30
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Software for running dynamics simulation of polymeric and mixed biomaterial (e.g hydrogels)
I was working on the development of a soft solid hydrogel having polymeric chains and molecules of different compounds dissolved in Phosphate Buffered Saline solution. There is a sub-study regarding ...
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32
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Van der Waals Parameters (non-bonded parameter) in Amber? [duplicate]
I have a complex that contains transition metals. I am doing parametrization and building the force field.
I have one question about the frcmod file.
In the file,
...
4
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0
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118
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Schrodinger operator with matrix potential and Green's function
Clearly Schrodinger operators with matrix potentials appear very naturally in molecular dynamics/quantum chemistry, particularly when considering a crude adiabatic basis or diabatic basis for an ...
8
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2
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660
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Practical use of the partition function in molecular simulations
In the second chapter of Understanding Molecular Simulation, Frenkel and Smit derive an equation for the partition function and the thermal average of the generic observable A, stating that these ...
2
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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
1
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0
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52
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How much should I scan an aromatic dihedral?
Suppose I have a napthalene-like molecule (attached), and I would like to scan (relaxed) its aromatic dihedral (highlighted atoms). I used CGENFF to obtain its dihedral parameters as follows,
HGA4 ...
- 11
2
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140
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How are class II force field cross-terms derived?
In some class II force fields, there are cross-terms that characterize bond-bond, bond-angle interactions and others. Example of equations below:
$$\sum_{bond-bond}^{}k_{bb}(b-b_{0})(b^{'}-b^{'}_{0})$$...
- 321
1
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1
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212
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Calculating self-diffusion coefficient from MSD programmatically
According to the Einstein relationship, the diffusion coefficient $D$ is
$$\lim _{t\rightarrow \infty} \frac{\langle \left(\mathbf{r}(t)-\mathbf{r}(0) \right) ^2\rangle}{6t} = D$$
I have run a MD ...
- 219
3
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1
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219
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Determining the torsion energy profile of butadiene by molecular dynamics
Disclaimer: this question is related to my previous question, although it is much more detailed
Consider the following rotation of butadiene:
I want to determine the relative energy of each dihedral ...
- 1,618
0
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1
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125
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Fixing incongruities in PES Scan [closed]
I tried to parameterize a particular x-y-z-t dihedral angle of novel molecule using a Quantum Mechanical scan, but I got the strange result below.
The energy changes sharply around 130° and $E_\text{...
- 11
1
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1
answer
78
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Help with molecular dynamics and computational modelling to check validity of hypothesis regarding SN2 reaction mechanisms [closed]
Polar aprotic solvents have a less hindered electronegative atom pointing out, namely oxygen, fluorine, and nitrogen, all of which have lone pairs besides having a partial negative charge. Now, all ...
4
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1
answer
228
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Tools for Molecular Simulation
I am a high school student and I don't know a whole lot about molecular simulation. I wish to view different conformers of cyclohexane and the changes that occur when substituents are attached (for ...
- 167
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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, ...
- 438
3
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0
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192
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Simple sandbox software for an interactive molecular dynamics simulation
I'm not sure if this is the right site to ask a such question. But I'm getting to learn the world of the small.
I know there is software out there like NAMD, and LAMMPS. But these tools are very ...
user86510
-1
votes
1
answer
970
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Using AutoDock Vina to dock multiple ligands to multiple receptors?
I am trying do that what the title depicts, but I keep running into errors creating the executable script. Is it even possible to automate the docking of multiple ligands to multiple receptors?
...
- 27
1
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1
answer
169
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How to calculate size of a specific cavity in a protein for every frame in trajectory file?
Here is the situation, I have trajecory file of a protein of interest. That protein has 2 main cavities that are participating in interraction with ligands or other proteins and also other cavities. ...
- 139
10
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1
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503
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Cloud-based molecular modeling software
I’m an IT Acquisitions and Licensing specialist researching well-supported cloud software alternatives to Fujitsu’s molecular modeling SCiGRESS. I am coming in with a tech background, but little to ...
- 117
5
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1
answer
245
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Building an average model from MD snapshots
I am performing a molecular dynamics simulation, and I am taking "snapshots" of the system at regular intervals.
The aim is that of finding the preferred geometry of a molecule in solution.
Are you ...
user32223
1
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1
answer
151
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Computational Efficiency of Periodic Boundary Conditions
From what I understand, in a molecular dynamics simulation the number of molecules included is limited by the computational power available.
In order to simulate macroscopic properties, one needs to ...
- 884
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
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106
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Why the use of MD simulations is less popular for the study of carbohydrates?
In classical all-atom MD simulations, the force fields for proteins, nucleic acids and lipids seem to be more well developed than carbohydrates. It seems to me that the use of MD simulations is not so ...
- 329
3
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371
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Amber Force Field Improper Parameterization Huge Kb Problem
I am trying to parameterize a molecule. I know dihedrals and impropers are the same for Amber Force Field. (Source: http://archive.ambermd.org/201004/0334.html)
So, I did PET scan for improper and I ...
- 209
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297
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Amber paramfit "monomer (or ligand)" problem [closed]
I am trying to parameterize a novel molecule which has atoms not included gaff or parm force field. I finished parameterizing vdw-bond and angle force field. Also I did PES Scan for dihedrals and I ...
- 125
2
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1
answer
2k
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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 ...
- 73
1
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0
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185
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Calculating the free energy of separation in AMBER
I am currently busy with my master's research project and I'm trying to calculate the free energy of separation of two cellobiose molecules in ionic liquid, that is, calculate the free energy of ...
1
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1
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523
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Calculating the x, y and z distances between two molecules - AMBER (Molecular Dynamics)
I am interested in calculating the x,y and z distance between two molecules over a given simulation time. I know how to calculate the total (r) distance between them, but I want the distance between ...
2
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0
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358
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How to develop a Reactive Force Field (ReaxFF)? (Molecular simulation)
Currently, I am working on CO2 capture on Hydrotalcites as solid adsorbents. I want to run molecular simulations to analyse the behaviour of the material under different temperatures, pressures and ...
2
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1
answer
306
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What causes energy peaks during a molecular dynamics energy minimization?
I'm minimizing the energy of a protein with NAMD using the fixedatom feature. I put my protein in a water box, and I allow all atoms other than the protein backbone ...
- 139
1
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1
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98
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Separating two sugars according to their heavy atoms - Steered Molecular Dynamics
I am trying to separate two methyl-N,N'-diacetylchitobiose sugars using steered molecular dynamics in AMBER. I have tested out:
...
4
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0
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152
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What computational methods are available for predicting nanoparticle structure?
I'm a quantum chemist, and nearly every system I've ever cared about has been studied by DFT. However, I am currently trying to model the surface interactions on a nanoparticle around 100 nm in ...
- 51
7
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2
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965
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Force Constants for Angles From Gaussian To AMBER: which value should I put in the matrix equation?
I am trying to make a new force field in AMBER for a novel compound including boron (which does not exist in GAFF). For this, I calculated freq and I found bond force constants but I couldn't find ...
- 348
14
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4
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4k
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Why are MD (Molecular Dynamics) simulations performed at room temperature for the purposes of studying proteins?
All of the MD simulations which are cited in the literature seem to be performed at room temperature (~300 Kelvins), while enzymes are usually bioactive at body temperature (~310 Kelvins).
I am ...
- 455
6
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1
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1k
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How to write an entire trajectory into a single PDB file?
I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library.
With VMD if I do ...
- 924
6
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1
answer
101
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What types of energies can be determined by molecular dynamics in gas phase or explicit solvents?
For molecular dynamics in the gas phase I've seen that electronic energy can be determined and also decomposed in kinetic and potential energy. I've also seen that we can include ZPE. But can we ...
- 5,802
3
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0
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186
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Minimum image convention and the atom “seeing” itself
The minimum image convention in molecular dynamics can be stated as:
A particle in the central square must not interact with one of its neighbors in the central square and an image of this neighbor ...
- 131
3
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1
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729
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How can you simulate the effect of a solvent on a polymer in an MD simulation?
I'm doing a molecular dynamics simulation of polymer melts and I want to include the effect of a good/bad solvent on the melt. How can this be done?
My simulation models polymers using a bead-spring ...
- 139
4
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1
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310
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What is the "curse of dimensionality" in molecular dynamics?
The 'curse of dimensionality' or the 'bottleneck problem' in molecular dynamics is explained in page 5 and 6 of Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods by Dominic Marx and Jurg ...
- 53
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 ...
- 11
4
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206
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LAMMPS: MD simulation of molecules? [closed]
I need to do molecular dynamics simulation of cyclodextrine molecules for a project and I am searching for an open source solution that can be used. I found LAMMPS to be quite well maintained and ...
- 2,804