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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

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 ...


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, ...


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

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 ...


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 ...


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

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 ...


5

You might want to have a look at acpype which is compatible with GAFF and AMBER-based force fields and probably others.


5

The correct syntax is then the following: $gmx rdf -f ftraj.xtc -s ftraj.tpr -ref "name C1 C2 C3" -sel "name C1 C2 C3" -selrpos part_res_com -seltype part_res_com My thoughts were partially clarified after consulting the useful command gmx help selections positions where it is described that POSTYPE can be atom, res_com, res_cog, mol_com ...


5

Thanks to the generous time and comments of @ShoubhikRMaiti, I was able to recreate the simulation. The problem in my code was 2-fold: I was using the topology filed created by LigParGen, which had different charges on the C and H atoms in my simulation as in the paper. I did not think to check LigParGen's output, and that is my own fault. Also, I was using ...


5

This is actually a straightforward problem about unit conversions and careful manipulation based on the functional forms of the potential we want. To go from the Improper Torsion Parameters to the Improper Dihedral in GROMACS, simply do the following transformation on the amplitude: $\textrm{ampl}\times 4.184\times n/2~$ where 4.184 is the unit conversion ...


4

Following Nike and Tyberius's suggestions, I rewrite my comment into an answer. Firstly, it is obvious that when the volume of the simulation box is sufficiently large, then a significant fraction of the box must be gaseous. Secondly, note that the simulation box has a finite size, so that when the equilibrium pressure of the gas is sufficiently low, it may ...


4

Turns out that it works with a simple addition of -ntomp and -np flags in the last line. Though I still do not know the answer to why it wouldn't run if not for them, when it can work for the higher number of processors like 40 or 80. The edited script: #!/bin/bash #PBS -e errorfile.err #PBS -o logfile.log #PBS -l walltime=24:00:00 #PBS -l select=4:ncpus=6 ...


4

I think that there isn't one. As the cause of the magnetic properties are the electrons, and no MD codes consider the electrons, they are unable to simulate magnetism.


3

Did you check that the bulk structures are stable? If they are, then the Coulomb part should be working, and the problem might be in your model. This type of problem is actually relatively common. If you use potentials that have been fit for bulk materials i.e. perfect crystals, you're only studying a small range of the possible configuration space: the ...


3

Actually that depends on what you're trying to achieve with the simulation. Generally speaking the magnetic field is not much different from the electric field, therefore the effect can be incorporated with small changes to fix efield in LAMMPS to account for different constants. In fact, this was what we did in a paper some time ago. However, the effect of ...


3

I assume you by "ranking" you mean "sorting numerically" ... I don't think there is a general solution for this in gmx - unless you are ready to do some script writing yourself ... As a workaround ... in an older gmx version there used to be a tool called mk_angndx https://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-mk_angndx.html?...


2

Thermodynamics is being bossy? After discussions in the chatroom I don't see anything wrong with your simulation settings. I think the culprit is phase equilibria. Either your system wants to be in two phases, or, it wants to be a single phase but you are starting with a box size large enough (density low enough) that you start with two phases and even after ...


1

The error is due that 9AZR is not a standard residue name. I recommend you to use the web services CHARMM-GUI. In the left menu, go to Input Generator. There you can generate the topology file as well the input files for different molecular dynamics software (including NAMD, GROMACS, etc.)


1

There are two options here and the choice depends on what you intend to do with your results. If you are going to perform QM calculations after MD, then you can just alter the charges as you outlined in your question. This is because QM will correct any issues you might come across. However, you need to make sure the molecule will behave in the manner in ...


1

You can calculate the Raman spectra by using VASP and Phonopy assisted python package. Check all the details here: vasp-raman


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