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15

What is a force field? The Wikipedia entry on this is a good resource, but I'll give my own description below. In the context of molecular dynamics (MD), a force field is one way of describing the interactions between atoms. In classical MD, the motion of atoms is determined by the instantaneous forces acting on the atoms (i.e., we need forces in order to ...


12

Which is more appropriate for the binding energy? Neither. Obi-Wan voice: "These are not the energies you're looking for." If I understand your goal, you're trying to compare two ligands and determine which is better at binding to a given protein (and, ideally, quantify "how much better" one is compared to the other). If that is the case, ...


11

Since you seem to have at least a start on automating the process of modifying the file, I will just address the other two parts of your question: the format of the nonbond_params section of a GROMACS .itp file and the meaning of the symbols used in the Martini force field. GROMACS format This is given in the GROMACS manual. To summarize: Atom1 Atom2 Func ...


11

I'm not sure why you would use radius for gyration as a measure of solubility. Radius of gyration roughly measures how "unfolded" (or more accurately, how "stretched out") a polymer is. Although this may correspond to a higher solvent accessible surface area (which can itself be calculated and is useful in some cases), it has nothing to ...


10

I am not a GROMACS user, but have used it once or twice during my course. As far as I can remember and understand, it is common to use different force field in MD if one simulate something solvated in something, e.g. formaldehyde (OPLSAA force field) in water (SPC,TIP3P, etc.). I guess we can also do that in GROMACS, but I do not really know how to specify ...


10

Don't Worry, it is not a problem, This happened because you used PBC (Periodic boundary condition) and VMD sometimes has bugs during the visualization in this case. The most important to you to see that the protein wasn't broken through all frames. You can solve this problem by using this command pbc unwrap -sel "protein" inside the Tk console as ...


9

So, with a lot of tries and errors I've found out how to perform such analysis. I'm using a library for Python called MDAnalysis. It can load Gromacs topologies and extract charges from them. Using them dipole moment for each molecule can be easily calculated and ordering parameters can be calculated from it. Here is the code. It may not be perfect, but it ...


9

Did you want to draw Si instead of S? Sulfur atoms bonded to two oxygens and two carbons, like the ones you have drawn here, are at least very rare, if not non-existent. It makes much better sense if what you want is to calculate the molecule with silicons instead of sulfurs, since that will be a silicone oligomer, which looks much more natural than the ...


8

Running simulations with small molecules is one thing that I found quite difficult especially because most online guides/tutorials are focused on proteins. So, here's a rough idea of what to do: Getting forcefield parameters: Your question is about this, so I will give a detailed explanation. There are many forcefields to choose from, e.g. MMFF94, UFF, ...


8

I believe I have figured it out. For those trying to martinize their all-atom files into coarse grain representations for martini 3, use the following package: https://github.com/marrink-lab/vermouth-martinize With respect to modifying the water for IDP simulations, I pulled out the W, SW and TW interactions from the martini v3.0.0 forcefield, like so: W ...


8

Is there an option in gmx mdrun to specify where to write the .xtc file? For example I want to specify specific directory path with large disk space. When you use the -deffnm md argument to gmx mdrun, it is assumed that all of the files will have the base name of md, so gromacs looks for md.tpr as input, and it writes md.xtc, md.edr etc. as output files in ...


7

Here's an approach calculating it by hand with numpy. The coordinates are loaded from the trajectory using mdtraj in python: #imports: import mdtraj as md import numpy as np import matplotlib.pyplot as plt #load trajectory: traj = md.load('traj.dcd', top='solvated.pdb') ##You would write this: ##traj = md.load_xtc('md.xtc', top='top.gro') #select oxygen ...


7

Short answer I am a regular GROMACS user. I do not think you can just easily have the total functional form "printed out" from GROMACS. However, you can obtain it from the topology file (top and itps) and the mdp file. Let me elaborate a little below. Longer answer The functional forms you are referring to in the GROMACS top/itp file are the ones used in ...


7

There is certainly Lammps, which has a fix efield that allows you to apply electric field in your chosen cartesian direction. But I am not sure if it works for your purposes. You can play around with it to see. https://lammps.sandia.gov/doc/fix_efield.html


7

This is a question that cannot have a "right" answer. As mentioned in the comments, the answer would depend on the experimental system and on the specific properties you want to reproduce. Since most experimental systems are in what is known as the "scaling regime" you probably need long polymers to begin with (I commented on the issue ...


7

You can do it either way. You need to give predocked files to GROMACS/Amber for running protein-ligand complex molecular simulations. Also have a look at HADDOCK web server for predocking. Place the receptor outside the interaction range of your protein (randomly) and run an MD simulation, to find the binding regions. But you need to do multiple MD runs to ...


7

The term's origin goes back to vector field which is a function that returns a vector for any given point in space (as in the image below on the left). We can almost "see" that such fields exist, by putting iron filings and a magnet on a sheet of paper (the magnetic field causes the iron filings to move accordingly): In classical molecular ...


7

The key thing to remember is that while a "proper" torsion includes atoms 1-2-3-4 with bonds between 1-2, then 2-3, and then 3-4, an improper torsion is just defined by any set of 4 atoms. So here's a proper torsion C-C-C-H in benzene: If I want the ring to be flat, I'd define this torsion to be, e.g. ±180° But I don't need to have four atoms ...


7

First, You need to click on Create Rep and you will get a new line in the box below as the picture attached (with the same name "protein" in your case). To show the ligand, you should know the name of your ligand, to ensure about your ligand name, you can choose in the keyword "resname" and all the resname will appear in the value box. Or ...


7

Note: there's nothing specific to Gromacs in the answer below. These are just shell scripting techniques that are relevant to any program that takes input from stdin. For cases where I know that colleagues have needed this with Gromacs, we've used the first option listed below (heredoc). FWIW, I didn't test either of these with Gromacs, but they should work. ...


7

How about this, also writes to a log file. This selects both group 1 and group 13 and write the indices to a index file (index.ndx) echo -e "1|13\nq"| gmx make_ndx -f em.gro -o index.ndx|& tee -a youlogfile.log


7

You need the chemical potential to do solubility The problem with solubility of large molecules, is that you need to know the chemical potential in the liquid and the solid. You can use Free Energy calculations to get the residual contribution to the chemical potential in the liquid, but, the residual contribution to the chemical potential of the solid is ...


6

This book by Klaus Schulten is detailed and explains concepts with examples from NAMD and visulaization from VMD.


6

I fear that GROMACS may not be able to capture the interaction you are talking about (If someone is an expert in GROMACS please correct me). This sort of pi-stacking interaction will likely result in either a charge transfer (if asymmetric) or some sort of pi-pi bonding interaction that a forcefield is unlikely to capture. If you took a snapshot of the MD ...


6

As I had previously written in the comments, the warning given by gromacs seems to indicate that the GROMOS force fields should not be used due to wrong parameterization: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct ...


6

Large pressure fluctuations are normal for nanoscale simulations of aqueous solutions (and other condensed systems without a gas phase). Pressure fluctuations are usually enormous in simulations of aqueous solutions because water is nearly incompressible. Let's say your system is a cube of water $(2~\mathrm{nm})^3$. Smaller systems will have larger ...


6

Snapshot types in OpenPathSampling depend on the type of engine you're using. To some extent, snapshot types can be interchanged (if you had OpenMM available, I think the approach you're trying would work), but the OPS Gromacs engine has some different internals. The Gromacs engine in OpenPathSampling mainly uses externally-defined trajectories (that is, ...


6

Docking and Molecular dynamics are two very different process. In docking, you will need the ligand (normally in a separate file), the protein (can be in a separate file too), and the information about the site where you want to dock the ligand. This information can be some residues or simple a (x,y,z) coordinate. Then the docking program will generate a ...


6

Molecular dynamics is based in Molecular Mechanics. Molecular Mechanics do many approximations in order to treat the atomic/molecular system. A good definition can be seen here: Molecular Mechanics is a computational method that computes the potential energy surface for a particular arrangement of atoms using potential functions that are derived using ...


6

I'd use OpenMM's openmmforcefields package, which is available on GitHub. I haven't used it extensively, but I recommended to a student in a colleague's lab and they've found it useful. Small molecule force fields: GAFF 1.x and 2.x parameters OpenFF parameters Biomolecule force fields: Amber-type (albeit not Amber ff19SB yet) CHARMM-type And it will, if ...


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