![]() ![]() This shows rigid molecules given both translational and rotational velocity by the velocity command and undergoing changes in direction and orientation upon impact with other molecules. norot_issue_mod_nodeform.avi: trajectory of the in.norot_issue_mod_nodeform input file ( _norot_mod_nodeform.lammpstrj) using fix rigid (this is the only difference with the preceding input).This shows rigid molecules given only translational velocity by the velocity command and undergoing only translation upon impact with other molecules norot_issue_nodeform.avi: trajectory of the in.norot_issue_nodeform input file ( _norot_nodeform.lammpstrj) using fix rigid/nve.I ran these scripts with and no issue related to defining fix deform before pair_style granular occurred.Īs suggested, I also tested similar input scripts by deleting the fix deform and creating an initial velocity and obtained similar results (enclosed): This shows rigid molecules undergoing both translation and rotation as expected. norot_issue_mod.avi: trajectory of the in.norot_issue_mod input file ( _norot_mod.lammpstrj) using fix rigid (this is the only difference with the preceding input).This shows rigid molecules undergoing only translation norot_issue.avi: trajectory of the in.norot_issue input file ( _norot.lammpstrj) using fix rigid/nve.To better illustrate the issue, I herein enclose a few VMD movies of the different simulations (10000 steps): For the norot_issue scripts, changing only fix rigid to fix rigid/nve results in distinct behavior. I initially included both for demonstration purposes but we could narrow the focus on the "issue" ones to illustrate the problem. The "no_issue" and "issue" input are indeed dramatically apart in terms of physical setup. tilt: cosine of the rotation orthogonal to a given axis.Thank you for taking the time to continue investigating.spinAngle: angle of rotation around a given axis.orientationProj: cosine of the angle of rotation from reference coordinates.orientationAngle: angle of rotation from reference coordinates.orientation: orientation from reference coordinates.inertiaZ: total moment of inertia of a group of atoms around a chosen axis.inertia: total moment of inertia of a group of atoms.gyration: radius of gyration of a group of atoms.eigenvector: projection of the atomic coordinates on a vector.rmsd: root mean square displacement (RMSD) from reference positions.selfCoordNum: coordination number between atoms within a group.coordNum: coordination number between two groups.dihedral: torsional angle between four groups.dipoleAngle: angle between two groups and dipole of a third group.cartesian: vector of atomic Cartesian coordinates.distancePairs: set of pairwise distances between two groups.distanceInv: mean distance between two groups of atoms.distanceDir: distance unit vector between two groups.distanceVec: distance vector between two groups.distanceXY: modulus of the projection of a distance vector on a plane.distanceZ: projection of a distance vector on an axis.distance: center-of-mass distance between two groups.Collective variable components (basis functions).Performance a Colvars calculation based on group size.Treatment of periodic boundary conditions.Selecting atoms for colvars: defining atom groups.Statistical analysis of collective variables.General options for a collective variable.Defining collective variables and their properties.Configuration syntax for the Colvars module.General parameters and input/output files.Collective Variables Interface (Colvars).Coloring Trick - Override a Coloring Category.Creating a set of black-and-white color definitions.Using the Python interpreter within VMD.Implicit Ligand Sampling ( volmap ils command).Turn off highlighting / Change highlight style.Selecting residues by clicking on the 3-D structure.Selecting residues from the Sequence window listing.Display Menu and Display Settings Window. ![]() Using the Joystick in the Graphics Window.Using the Spaceball in the Graphics Window.Tracking Script Command Versions of the GUI Actions.Parallel Computing on Clusters and Supercomputers.Basic Hardware and Software Requirements.VMD development is supported by the National Institutes of Health Use the scripting interfaces for analysis and to This guide documents the user interfacesĭisplaying and grapically manipulating molecules, and describes how to How to run and use the molecular visualization and analysis University of Illinois at Urbana-Champaign pdb in VMD and execute: 1) set sel atomselect top. NIH Biomedical Research Center for Macromolecular Modeling and Bioinformaticsīeckman Institute for Advanced Science and Technology Hi Najme, You can also use VMD software to calculate the center of mass. ![]()
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