To translate, hit the 't' key while the cursor is in the display window.


It is developed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign. Using the spin state of nitrogen-vacancy (NV) defect centers in diamond to probe magnetic fields is an attractive prospect.


You could use the gmx trjconv command to make your protein and ligand to the center of the box and fit all atoms to a reference structure.

. . Thus, when a molecule leaves the box in one direction, it re-enters the box on the opposite side.

Select the Center menu item and pick one atom at one of the ends of the protein; The cursor should display a cross.

95 × 92. . 1)The REMARK section is for user comments.

We then move all the atoms so that the protein center-of-mass is in the center of the box. .


Save the visualization state of the system.

. 3) The index (serial number) of each atom.

Show three molecules side-by-side in VMD after aligning along a dihedral. How we can delete some molecules from box in vmd? I want to delete some solvent molecules in box after md production, but I don't the lables of them and how delete them and how I delete a specific molecule?? Hi, right click on the selected molecule and choose "delete molecule".


Hughes et al.


. . xtc file need command: trjconv -f md.

. 1. Hughes et al. . The grid size may be modified from that passed to the routine so that an integer grid dimension fits the dimensions of the box containing the molecule.

We must move the CSO along a vector from the center-of-mass of the molecule to the origin.

(Western Regional Research Center, Agricultural Research Service, U. Feb 11, 2023 · Subsequently, superposition models were prepared by VMD (v1.


4” to “1.


Simple dynamic analysis via labels.

The Clone representations window will pop up.