Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2023 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #include "Colvar.h"
      23             : #include "core/PlumedMain.h"
      24             : #include "ActionRegister.h"
      25             : #include "tools/PDB.h"
      26             : #include "reference/DRMSD.h"
      27             : #include "reference/MetricRegister.h"
      28             : #include "core/Atoms.h"
      29             : 
      30             : namespace PLMD {
      31             : namespace colvar {
      32             : 
      33             : //+PLUMEDOC DCOLVAR DRMSD
      34             : /*
      35             : Calculate the distance RMSD with respect to a reference structure.
      36             : 
      37             : To calculate the root-mean-square deviation between the atoms in two configurations
      38             : you must first superimpose the two structures in some ways.  Obviously, it is the internal vibrational
      39             : motions of the structure - i.e. not the translations and rotations - that are interesting. However,
      40             : aligning two structures by removing the translational and rotational motions is not easy.  Furthermore,
      41             : in some cases there can be alignment issues caused by so-called frame-fitting problems. It is thus
      42             : often cheaper and easier to calculate the distances between all the pairs of atoms.  The distance
      43             : between the two structures, \f$\mathbf{X}^a\f$ and \f$\mathbf{X}^b\f$ can then be measured as:
      44             : 
      45             : \f[
      46             : d(\mathbf{X}^A, \mathbf{X}^B) = \sqrt{\frac{1}{N(N-1)} \sum_{i \ne j} [ d(\mathbf{x}_i^a,\mathbf{x}_j^a) - d(\mathbf{x}_i^b,\mathbf{x}_j^b) ]^2}
      47             : \f]
      48             : 
      49             : where \f$N\f$ is the number of atoms and \f$d(\mathbf{x}_i,\mathbf{x}_j)\f$ represents the distance between
      50             : atoms \f$i\f$ and \f$j\f$.  Clearly, this representation of the configuration is invariant to translation and rotation.
      51             : However, it can become expensive to calculate when the number of atoms is large.  This can be resolved
      52             : within the DRMSD colvar by setting LOWER_CUTOFF and UPPER_CUTOFF.  These keywords ensure that only
      53             : pairs of atoms that are within a certain range are incorporated into the above sum.
      54             : 
      55             : In PDB files the atomic coordinates and box lengths should be in Angstroms unless
      56             : you are working with natural units.  If you are working with natural units then the coordinates
      57             : should be in your natural length unit.  For more details on the PDB file format visit http://www.wwpdb.org/docs.html
      58             : 
      59             : \par Examples
      60             : 
      61             : The following tells plumed to calculate the distance RMSD between
      62             : the positions of the atoms in the reference file and their instantaneous
      63             : position. Only pairs of atoms whose distance in the reference structure is within
      64             : 0.1 and 0.8 nm are considered.
      65             : 
      66             : \plumedfile
      67             : DRMSD REFERENCE=file1.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8
      68             : \endplumedfile
      69             : 
      70             : The reference file is a PDB file that looks like this
      71             : 
      72             : \auxfile{file1.pdb}
      73             : ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H
      74             : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C
      75             : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H
      76             : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H
      77             : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O
      78             : END
      79             : \endauxfile
      80             : 
      81             : The following tells plumed to calculate a DRMSD value for a pair of molecules.
      82             : 
      83             : \plumedfile
      84             : DRMSD REFERENCE=file2.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8 TYPE=INTER-DRMSD
      85             : \endplumedfile
      86             : 
      87             : In the input reference file (file.pdb) the atoms in each of the two molecules are separated by a TER
      88             : command as shown below.
      89             : 
      90             : \auxfile{file2.pdb}
      91             : ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H
      92             : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C
      93             : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H
      94             : TER
      95             : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H
      96             : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O
      97             : END
      98             : \endauxfile
      99             : 
     100             : In this example the INTER-DRMSD type ensures that the set of distances from which the final
     101             : quantity is computed involve one atom from each of the two molecules.  If this is replaced
     102             : by INTRA-DRMSD then only those distances involving pairs of atoms that are both in the same
     103             : molecule are computed.
     104             : 
     105             : */
     106             : //+ENDPLUMEDOC
     107             : 
     108             : 
     109             : class DRMSD : public Colvar {
     110             : 
     111             :   bool pbc_;
     112             :   MultiValue myvals;
     113             :   ReferenceValuePack mypack;
     114             :   std::unique_ptr<PLMD::DRMSD> drmsd_;
     115             : 
     116             : public:
     117             :   explicit DRMSD(const ActionOptions&);
     118             :   void calculate() override;
     119             :   static void registerKeywords(Keywords& keys);
     120             : };
     121             : 
     122       10442 : PLUMED_REGISTER_ACTION(DRMSD,"DRMSD")
     123             : 
     124          13 : void DRMSD::registerKeywords(Keywords& keys) {
     125          13 :   Colvar::registerKeywords(keys);
     126          26 :   keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure and the atoms involved in the CV.");
     127          26 :   keys.add("compulsory","LOWER_CUTOFF","only pairs of atoms further than LOWER_CUTOFF are considered in the calculation.");
     128          26 :   keys.add("compulsory","UPPER_CUTOFF","only pairs of atoms closer than UPPER_CUTOFF are considered in the calculation.");
     129          26 :   keys.add("compulsory","TYPE","DRMSD","what kind of DRMSD would you like to calculate.  You can use either the normal DRMSD involving all the distances between "
     130             :            "the atoms in your molecule.  Alternatively, if you have multiple molecules you can use the type INTER-DRMSD "
     131             :            "to compute DRMSD values involving only those distances between the atoms at least two molecules or the type INTRA-DRMSD "
     132             :            "to compute DRMSD values involving only those distances between atoms in the same molecule");
     133          13 : }
     134             : 
     135          12 : DRMSD::DRMSD(const ActionOptions&ao):
     136          12 :   PLUMED_COLVAR_INIT(ao), pbc_(true), myvals(1,0), mypack(0,0,myvals)
     137             : {
     138             :   std::string reference;
     139          12 :   parse("REFERENCE",reference);
     140             :   double lcutoff;
     141          12 :   parse("LOWER_CUTOFF",lcutoff);
     142             :   double ucutoff;
     143          12 :   parse("UPPER_CUTOFF",ucutoff);
     144          12 :   bool nopbc(false);
     145          13 :   parseFlag("NOPBC",nopbc);
     146          12 :   pbc_=!nopbc;
     147             : 
     148          12 :   addValueWithDerivatives(); setNotPeriodic();
     149             : 
     150             :   // read everything in ang and transform to nm if we are not in natural units
     151          12 :   PDB pdb;
     152          24 :   if( !pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()) )
     153           1 :     error("missing input file " + reference );
     154             : 
     155             :   // store target_ distance
     156          11 :   std::string type; parse("TYPE",type);
     157          22 :   drmsd_=metricRegister().create<PLMD::DRMSD>( type );
     158          11 :   drmsd_->setBoundsOnDistances( !nopbc, lcutoff, ucutoff );
     159          11 :   drmsd_->read( pdb );
     160          11 :   checkRead();
     161             : 
     162             :   std::vector<AtomNumber> atoms;
     163          11 :   drmsd_->getAtomRequests( atoms );
     164             : //   drmsd_->setNumberOfAtoms( atoms.size() );
     165          11 :   requestAtoms( atoms );
     166             : 
     167             :   // Setup the derivative pack
     168          11 :   myvals.resize( 1, 3*atoms.size()+9 ); mypack.resize( 0, atoms.size() );
     169         129 :   for(unsigned i=0; i<atoms.size(); ++i) mypack.setAtomIndex( i, i );
     170             : 
     171          11 :   log.printf("  reference from file %s\n",reference.c_str());
     172          11 :   log.printf("  which contains %d atoms\n",getNumberOfAtoms());
     173          11 :   log.printf("  with indices : ");
     174         129 :   for(unsigned i=0; i<atoms.size(); ++i) {
     175         118 :     if(i%25==0) log<<"\n";
     176         118 :     log.printf("%d ",atoms[i].serial());
     177             :   }
     178          11 :   log.printf("\n");
     179          28 : }
     180             : 
     181             : // calculator
     182         595 : void DRMSD::calculate() {
     183             : 
     184         595 :   double drmsd; Tensor virial; mypack.clear();
     185         595 :   drmsd=drmsd_->calculate(getPositions(), getPbc(), mypack, false);
     186             : 
     187         595 :   setValue(drmsd);
     188        9285 :   for(unsigned i=0; i<getNumberOfAtoms(); ++i) { if( myvals.isActive(3*i) ) setAtomsDerivatives( i, mypack.getAtomDerivative(i) ); }
     189         595 :   setBoxDerivatives( mypack.getBoxDerivatives() );
     190         595 : }
     191             : 
     192             : }
     193             : }