Position restraints via zero|mass dummy atoms

Position restraints via zero|mass dummy atoms · Issue

Position restraints via zero-mass dummy atoms · Issue #2262 - GitHub

I can explain what we did in yank when we wanted to restrain some protein atoms to reference positions for a quick alchemical scouting protocol.

Position restraints of positions relative to moving center of mass

I want to pull the center of mass of a group of atoms in x-direction by using the harmonic potential, but I also want each atom in the group to stay static.

namd-l: Re: Colvars Restraint Question

If you depend on absolute positions, yeah, its a problem. But ... protein-bilayer system and then a dummy atom...? In the group with ...

Setting up a virtual site to represent a dummy(=massless) LJ sphere

... using position restraints and such, and then use a [ nonbond_params ] section. ... Why not use an actual dummy atom with some mass, and/or ...

Dummy atoms and constrained geometry optimization - Q-Chem Talk

My current understanding is the real atoms are numbered by their positions in the z matrix, and the dummy atoms then start at one more than the ...

GROMACS: Best restraint to keep ions out of the pore?

There are other fancier ways to implement these restraints, e.g., you may put a repulsive potential via a dummy atom in the center of the ...

namd-l: Re: use of colvars to restrain the absolute positions of all ...

Conversely, there are ways you can calculate the restraint free energy, even for NAMD's built-in restraints, through post-processing of the trajectory: it is ...

Section 1: Prepare the system and set up the restraints

To set up restraints, we need to pick five atoms: three atoms on the host and two atoms on the guest. For the host, we will choose heavy atom C11, C23 and C51 ...

[gmx-users] Distance restrain with dummy atom - KTH

... position > restraint simulation, where flat-bottomed position restraint applied on > water and ions . The topology file looks as shown below ...

Restraints, Constraints and Group Fitting, and Disorder

1. Constraints for the coordinates and anisotropic displacement parameters for atoms on special positions: these are generated automatically by the program for ...

Restrained structure-factor least-squares refinement ... - IUCr Journals

A novel way of restraining groups of atoms to be planar has been developed that does not require dummy atoms and does not restrain the plane to lie in its ...

Dummy Atoms in Alchemical Free Energy Calculations

Obviously, one needs to pay attention that this modified energy term positions the dummy atom in the correct geometry. Proceeding in this manner ...

The Coot User Manual - MRC Laboratory of Molecular Biology

-> Peptide Restraints… Next: Moving Zero Occupancy Atoms, Previous: Planar ... dummy atom at the pointer position. Use an argument of 0 to revert to ...

Magnesium-Cationic Dummy Atom Molecules Enhance ...

... using restraints. The combination of quantum mechanical and molecular ... Attaching cationic dummy atoms to the central metal atom at defined positions ...

[gmx-users] dummies and positional restraints

So you are sure you have included the restraints in the dummy topology. What is the position restraint energy then? If I saw it correclty you only restrain ...

Implementing a Harmonic Length Restraint for Linear Molecules

For atom types 2 through n, this restraining force will have a negative contribution of k times (total length of the molecule the given atom ...

6 Restraints, constraints and rigid bodies - De Gruyter

The most basic restraint would be to prevent atoms getting too close using the ... cases it can be convenient to place a dummy atom with zero occupancy at the ...

RestraintMaker: a graph-based approach to select distance ... - NCBI

In addition, a user-defined cutoff distance d res between the pairs of atoms is introduced (here, d res = 0.1 nm ). Therefore, a possible distance restraint is ...

Restraints - GROMACS 2024.2 documentation

Using three different force constants the position restraints can be ... Position restraints are applied to a special fixed list of atoms. Such a ...

Colvars Module - Reference Manual

block defines a hydrogen bond, implemented as a coordination number (eq. 3) between the donor and the acceptor atoms. Therefore, it accepts the ...