VMD patches

Visual Molecular Dynamics (VMD) is a molecular visualization program developed by the University of Illinois at Urbana-Champaign (UIUC).

This repository includes contributions that are not (yet) part of the VMD distribution.

To comply with the UIUC license, only patches are distributed but not the original files. For ease of distribution, the patches are available under the open-source LGPL license: however, the code that they provide is meant to be included in VMD.

If a certain diff file is empty, it means that the corresponding change has been already merged into the current development version of VMD. Nonetheless, test or example files are retained after merging for comparison against older VMD versions.

The following patches are included in this repository:

• c++11: This patch enables building VMD with the C++11 standard, allowing to include in the resulting build newer code that requires it (see list of list of C++11 features in the Colvars module).

  Status: not included in the main VMD distribution yet; a patch is available for the VMD CVS snapshot of date 2022-05-13.

• lepton: This patch adds a new LEPTON flag in the configure script to link VMD against the Lepton library, which is distributed under the MIT license and its reference version is available from the OpenMM package. In Colvars, Lepton is used to implement the customFunction feature.

The source code of the Lepton library should be copied into lib/lepton and a corresponding static library built accordingly. On a Linux or macOS machine, feel free to use the add_lepton.sh script to automate these steps using Git and CMake. Alternatively, you may copy a pre-compiled Lepton library into lib/lepton/lib_$config_arch before building VMD.

Please also apply the c++11 patch.

Status: not included in the main VMD distribution yet; a patch is available for the VMD CVS snapshot of date 2022-05-13.

• volmap-fix: This change fixes a bug in the volmap utility when dynamic selections are used (i.e. when the set of atoms changes between trajectory frames). Files in this folder allow to compare behavior with different VMD versions; because the bug is caused by an out-of-bounds memory access, it is advisable to repeat the test a few times.

  Status: included in VMD CVS since 2019-01-23, patch available for VMD 1.9.3 in the v1.9.3 branch.

The standard Unix method can be used to update a VMD source tree:

patch -p1 < patch-name.diff -d VMD-source-top-directory

patch is a standard utility in Linux and MacOS, also available on Windows via the UnxUtils package.

See also the README of the Colvars repository to update VMD with the latest version of the Colvars module.

Please see here for instructions about how to compile VMD from source.