9 votes

How to identify small molecules in a structure without bonds

I used OpenBabel with the --separate option. From the documentation: --separate Separate disconnected fragments into individual ...
Camps's user avatar
  • 23.3k
7 votes

How to identify small molecules in a structure without bonds

You ask for either software or algorithm. Other answers speak to existing software. The underlying algorithms generally revolve around interatomic distances. For instance, one chooses a suitable ...
John Bollinger's user avatar
5 votes

How to add atom attribute molecule for each layer in LAMMPS?

I accepted Andrey Poletayev's answer and upvoted it because it gives me the right direction, although it needs to be corrected (see my comment). However, I couldn't do it with the python package ASE, ...
Vladislav Gladkikh's user avatar
5 votes

Restrain a protein to be helical in an MD simulation

Applying restraints to keep a specific secondary structure is common/mandatory when using coarse grained force fields for MD simulations, try searching for simulations with the MARTINI force field.
Frank Jensen's user avatar
  • 1,776
4 votes
Accepted

Restrain a protein to be helical in an MD simulation

The general method is to constrain the CA atoms of the protein while you are equilibrating the structure. You can do this in gromacs by creating a posres.itp file that has all the CA atoms, and then ...
Hemanth Haridas's user avatar
4 votes
Accepted

Hydrogen bonding autocorrelations

This is the methodology that I used to compute continuous hydrogen bond autocorrelation function. I had 21 nucleobases in my system, and the code is written according to it, but should be extendable ...
Hemanth Haridas's user avatar
4 votes
Accepted

How to add atom attribute molecule for each layer in LAMMPS?

The 'molecule' identifier will need be a separate column field for each atom. In your case, each layer will count for one molecule. So layer 1 will have a 1 in that column and so on. From the ...
Andrey Poletayev's user avatar
3 votes

Optimum number of CPUs to use for an efficient LAMMPS simulation

Choosing the optimal number of processors is heavily dependent on many things: number of atoms (more atoms tends to allow more processors to be used) chosen algorithm (algorithms with more numerics ...
nickpapior's user avatar
  • 3,316
3 votes

How to identify small molecules in a structure without bonds

You can use some clustering algorithm, or a mixture model. E.g., in Julia: using Clustering This will import the Clustering.jl library. Then, a function to read ...
Vladislav Gladkikh's user avatar
2 votes

How to identify small molecules in a structure without bonds

For the task I recommend OpenBabel and a subsequent query on PubChem with PubChemPy. The "dictionary of chemical compounds" used hence is the one by NIH presuming compounds of your cluster ...
robert's user avatar
  • 23
2 votes

Hydrogen bonding autocorrelations

Do you have any opinions on these codes? does not seem like a useful question to me. My opinion might be that those codes are the most beautiful thing ever written, but I might also be someone with ...
Shern Ren Tee's user avatar
2 votes
Accepted

Problem with 'Thermo and fix ave not computed at compatible times' in LAMMPS

You seem to be using your fix f_ave, which gets computed every 1000 steps, in your thermo_style output, which is written every ...
Andrey Poletayev's user avatar
1 vote

Hydrogen bonding autocorrelations

I noticed you've selected Hemanth's answer. However, I've devised my code differently and would like to verify if it generates the same results as yours. To do so, I need a reference. Could you please ...
Abd-Elazeem Mohamed's user avatar
1 vote

How to identify small molecules in a structure without bonds

You can use the RDKit package to parse your molecule and then iteratively check if a bond is present between each of the atoms. This would allow you to build a connectivity matrix, that you can store ...
Hemanth Haridas's user avatar

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