driver

This is part of the cltools module

driver is a tool that allows one to to use plumed to post-process an existing trajectory.

The input to driver is specified using the command line arguments described below.

In addition, you can use the special READ command inside your plumed input to read in colvar files that were generated during your MD simulation. The values read in can then be treated like calculated colvars.

Warning

Notice that by default the driver has no knowledge about the masses and charges of your atoms! Thus, if you want to compute quantities depending charges (e.g. DHENERGY) or masses (e.g. COM) you should pass the proper information to the driver. You can do it either with the –pdb option or with the –mc option. The latter will read a file produced by DUMPMASSCHARGE .

The input trajectory is specified using one of the following

--ixyz	the trajectory in xyz format
--igro	the trajectory in gro format
--ixtc	the trajectory in xtc format (xdrfile implementation)
--itrr	the trajectory in trr format (xdrfile implementation)
--mf_dcd	molfile: the trajectory in dcd format
--mf_crd	molfile: the trajectory in crd format
--mf_crdbox	molfile: the trajectory in crdbox format
--mf_gro	molfile: the trajectory in gro format
--mf_g96	molfile: the trajectory in g96 format
--mf_trr	molfile: the trajectory in trr format
--mf_trj	molfile: the trajectory in trj format
--mf_xtc	molfile: the trajectory in xtc format
--mf_pdb	molfile: the trajectory in pdb format

The following must be present

--plumed	( default=plumed.dat ) specify the name of the plumed input file
--timestep	( default=1.0 ) the timestep that was used in the calculation that produced this trajectory in picoseconds
--trajectory-stride	( default=1 ) the frequency with which frames were output to this trajectory during the simulation
--multi	( default=0 ) set number of replicas for multi environment (needs mpi)

The following options are available

--help/-h	( default=off ) print this help
--help-debug	( default=off ) print special options that can be used to create regtests
--noatoms	( default=off ) don't read in a trajectory. Just use colvar files as specified in plumed.dat
--dump-full-virial	( default=off ) with –dump-forces, it dumps the 9 components of the virial

--length-units	units for length, either as a string or a number
--dump-forces	dump the forces on a file
--dump-forces-fmt	( default=%f ) the format to use to dump the forces
--pdb	provides a pdb with masses and charges
--mc	provides a file with masses and charges as produced with DUMPMASSCHARGE
--box	comma-separated box dimensions (3 for orthorombic, 9 for generic)
--natoms	provides number of atoms - only used if file format does not contain number of atoms

Examples

The following command tells plumed to postprocess the trajectory contained in trajectory.xyz by performing the actions described in the input file plumed.dat. If an action that takes the stride keyword is given a stride equal to \(n\) then it will be performed only on every \(n\)th frame in the trajectory file.

plumed driver --plumed plumed.dat --ixyz trajectory.xyz

The following command tells plumed to postprocess the trajectory contained in trajectory.xyz. by performing the actions described in the input file plumed.dat. Here though –trajectory-stride is set equal to the frequency with which frames were output during the trajectory and the –timestep is equal to the simulation timestep. As such the STRIDE parameters in the plumed.dat files are no longer ignored and any files output resemble those that would have been generated had we run the calculation we are running with driver when the MD simulation was running.

plumed driver --plumed plumed.dat --ixyz trajectory.xyz --trajectory-stride 100 --timestep 0.001

By default you have access to a subset of the trajectory file formats supported by VMD, e.g. xtc and dcd:

plumed driver --plumed plumed.dat --pdb diala.pdb --mf_xtc traj.xtc --trajectory-stride 100 --timestep 0.001

where –mf_ prefixes the extension of one of the accepted molfile plugin format.

To have support of all of VMD's plugins you need to recompile PLUMED. You need to download the SOURCE of VMD, which contains a plugins directory. Adapt build.sh and compile it. At the end, you should get the molfile plugins compiled as a static library libmolfile_plugin.a. Locate said file and libmolfile_plugin.h, and customize the configure command with something along the lines of:

configure [...] LDFLAGS="-ltcl8.5 -L/mypathtomolfilelibrary/ -L/mypathtotcl" CPPFLAGS="-I/mypathtolibmolfile_plugin.h/"

and rebuild.

Molfile plugin require periodic cell to be triangular (i.e. first vector oriented along x and second vector in xy plane). This is true for many MD codes. However, it could be false if you rotate the coordinates in your trajectory before reading them in the driver. Also notice that some formats (e.g. amber crd) do not specify atom number. In this case you can use the --natoms option:

plumed driver --plumed plumed.dat --imf_crd trajectory.crd --natoms 128

Check the available molfile plugins and limitations at http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/.

Additionally, you can use the xdrfile implementation of xtc and trr. To this aim, just download and install properly the xdrfile library (see here: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library). If the xdrfile library is installed properly the PLUMED configure script should be able to detect it and enable it. Notice that the xdrfile implementation of xtc and trr is more robust than the molfile one, since it provides support for generic cell shapes.