![]() ![]() The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.I haven’t found better way than this, I used a long time to figure out how to do this efficiently. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The conversion tool leverages the capabilities of VMD, particularly those found in the TopoTools plugin (see Supporting Information) to facilitate this. See the documentation for detailed usage. Then, in order to generate the data script I need for LAMMPS, I used the writelammpsdata command in TopoTools. Topotools plugins does provide you a method to read LAMMPS native data files. I tried using these files in VMD using the Add solvation box tool to generate the water box. Script requires TopoTools and pbctools package require topotools package require pbctools Load the data file and trajectory dcd set molid topo readlammpsdata data. But what I have are psf, pdb, topology and parameter files from NAMD. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. I’m trying to create a data script for TIP4P water molecule to be used in LAMMPS. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. ![]() the second step is to use the created selection to access the information about the atoms in the selections. topo writegmxtop structure.top list parameterfile1.prm parameterfile2. mol new structure.psf mol addfile structure.pdb Pass along a list of parameters to generate structure.top, suitable for preparing gromacs simulations. This is done by a function called atomselect, which returns the name of the new atom selection. package require topotools 1.6 Load the structure into VMD. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. selection given the selection text, molecule id, and optional frame number. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. TopoTools is a plugin for VMD providing a collection of Tcl commands to manipulate, build, read and write topologies (i.e. ![]() ![]() These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. ![]()
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