From 729dfc117b08cf2f6b01d28a0f51f14640d1d12d Mon Sep 17 00:00:00 2001 From: Carlo Camilloni <carlo.camilloni@gmail.com> Date: Mon, 2 Jun 2014 10:26:06 +0100 Subject: [PATCH] Group: some restructuring --- user-doc/Group.txt | 69 ++++++++++++++++++++++++++++++++++------------ 1 file changed, 52 insertions(+), 17 deletions(-) diff --git a/user-doc/Group.txt b/user-doc/Group.txt index 3dc061a3b..1dc2a15b5 100644 --- a/user-doc/Group.txt +++ b/user-doc/Group.txt @@ -17,19 +17,64 @@ predefined as \ref GROUP that can be reused multiple times. Atoms' list can be d - all the above methods together (i.e. GROUP ATOMS=1,2,10-20,40-60:5,100-70:-2 LABEL=g5). Note that some collective variable can only accept a fixed number of atoms, for example a \ref DISTANCE is calculated -using two atoms only. +using two atoms only, an \ref ANGLE is calcuated using either 3 or 4 atoms and \ref TORSION is calculated using 4 atoms. + +\subsection mols Molecules + +In addition, for certain colvars, pdb files can be read in using the following keywords and used to select ATOMS: + +@TOPOLOGY@ + +The information on the molecules in your system can either be provided in the form of a pdb file or as a set of lists of +atoms that describe the various chains in your system using \ref MOLINFO. If a pdb file is used plumed the MOLINFO command will endeavor to +recognize the various chains and residues that make up the molecules in your system using the chainIDs and resnumbers from +the pdb file. You can then use this information in later commands to specify atom lists in terms residues. For example using +this command you can find the backbone atoms in your structure automatically, or you can select automatically the torsion +angles of a protein. + +The following example shows how to use \ref MOLINFO with \ref TORSION: + +\verbatim +MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb +t1: TORSION ATOMS=@phi-3 +t2: TORSION ATOMS=@psi-4 +PRINT ARG=t1,t2 FILE=colvar STRIDE=10 +\endverbatim + +\subsection pbc Broken Molecules and PBC + +PLUMED is designed so that for the majority of the CVs implemented the periodic boundary conditions are treated +in the same manner as they would be treated in the host code. In some codes this can be problematic when the colvars +you are using involve some property of a molecule. These codes allow the atoms in the molecules to become separated by +periodic boundaries, a fact which PLUMED could only deal with were the topology passed from the MD code to PLUMED. Making this +work would involve a lot laborious programming and goes against our original aim of having a general patch that can be implemented +in a wide variety of MD codes. Consequentially, we have implemented a more pragmatic solution to this probem - the user specifies +in input any molecules (or parts of molecules) that must be kept in tact throughout the simulation run. In PLUMED 1 this was done +using the ALIGN_ATOMS keyword. In PLUMED 2 the same effect can be acchieved using the \subpage WHOLEMOLECULES command. + +The following input computes the end-to-end distance for a polymer of 100 atoms and keeps it at a value around 5. + +\verbatim +WHOLEMOLECULES ENTITY0=1-100 +e2e: DISTANCE ATOMS=1,100 NOPBC +RESTRAINT ARG=e2e KAPPA=1 AT=5 +\endverbatim + +Notice that NOPBC is used to be sure in \ref DISTANCE that if the end-to-end distance is larger than half the simulation box the distance +is compute properly. Also notice that, since many MD codes break molecules across cell boundary, it might be necessary to use the +\ref WHOLEMOLECULES keyword (also notice that it should be before distance). Notice that most expressions are invariant with respect to a change in the order of the atoms, but some of them depend on that order. E.g., with \ref WHOLEMOLECULES it could be useful to specify atom lists in a reversed order. -In addition, for certain colvars, pdb files can be read in using the following keywords: - -@TOPOLOGY@ +\verbatim +# to see the effect, one could dump the atoms as they were before molecule reconstruction: +# DUMPATOMS FILE=dump-broken.xyz ATOMS=1-20 +WHOLEMOLECULES STRIDE=1 ENTITY0=1-20 +DUMPATOMS FILE=dump.xyz ATOMS=1-20 +\endverbatim -The read in pdb files are used by PLUMED to define things like residues, the backbone atoms and so on. These can then be -used within the input to colvars to make inputting the lists of atoms involved more straightforward. Documentation for -how these shortcuts can be used can be found in the documentation for the various CVs. \section vatoms Virtual Atoms @@ -52,16 +97,6 @@ DISTANCE ATOMS=11,com1 If you don't want to calculate CVs from the virtual atom. That is to say you just want to monitor the position of a virtual atom (or any set of atoms) over the course of your trajectory you can do this using \ref DUMPATOMS. -\section mols Molecules - -PLUMED is designed so that for the majority of the CVs implemented the periodic boundary conditions are treated -in the same manner as they would be treated in the host code. In some codes this can be problematic when the colvars -you are using involve some property of a molecule. These codes allow the atoms in the molecules to become separated by -periodic boundaries, a fact which PLUMED could only deal with were the topology passed from the MD code to PLUMED. Making this -work would involve a lot laborious programming and goes against our original aim of having a general patch that can be implemented -in a wide variety of MD codes. Consequentially, we have implemented a more pragmatic solution to this probem - the user specifies -in input any molecules (or parts of molecules) that must be kept in tact throughout the simulation run. In PLUMED 1 this was done -using the ALIGN_ATOMS keyword. In PLUMED 2 the same effect can be acchieved using the \subpage WHOLEMOLECULES command. */ -- GitLab