#VMD INSTALLATION MOD#
usage: epock -s coor.pdb -c conf.cfg File I/O: -s Input Coordinate file (pdb format) -c Input Configuration file -f Input, Opt Trajectory file (gromacs xtc format) -o Output, Opt Volume output file (default: volume.dat) Options: -b First frame (ps) to read from trajectory -e Last frame (ps) to read from trajectory -ox Output cavity trajectory file (default: no) -dt Only use frame when t MOD dt = first time (ps) -martini Use martini vdW radii i.e. on the fly, which make them choice pretreatment tools.Įpock v1.0.0rc Calculates the volume of cavities along a trajectory.
Notably, these tools can also filter, centre, fit, deal with periodic boundaryĬonditions, etc. To as numerous output formats (see for example mdanalysis dcd2xtc.py script). Numerous tools and libraries that can convert MD trajectory formats have beenįor instance, Gromacs trjconv tool as well as the mdanalysis library can convert many input formats Trajectories to the Gromacs xtc format, saving terabytes of storage with Hence, our humble opinion is that NAMD users should probably convert their dcd More than three times lighter than in the equivalent NAMD dcd file format. This format nicely compresses floating point numbers, which makes its storage Hence, the Gromacs users community is very used to this format. The xtc format is Gromacs standard file format for trajectories. We chose this file format for several reasons. VMD plugin to benefit VMD I/O capacities.Įpock command-line tool reads Gromacs xtc (and trr) trajectory files. NAMD dcd file format among others, one could run Epock using its dedicated
Importantly, Epock can be used as a VMD plugin (see sectionĪs VMD can read numerous trajectory formats, including Gromacs xtc and The input trajectory format can be of crucial importance when it comes to One of Epock main purposes is to efficiently calculate pocket volume along MD
Epock trajectory formats and conversion ¶
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