Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.
       3             : 
       4             : See http://www.maze-code.github.io for more information.
       5             : 
       6             : This file is part of maze.
       7             : 
       8             : maze is free software: you can redistribute it and/or modify it under the
       9             : terms of the GNU Lesser General Public License as published by the Free
      10             : Software Foundation, either version 3 of the License, or (at your option)
      11             : any later version.
      12             : 
      13             : maze is distributed in the hope that it will be useful, but WITHOUT ANY
      14             : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
      15             : FOR A PARTICULAR PURPOSE.
      16             : 
      17             : See the 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 maze. If not, see <https://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : 
      23             : /**
      24             :  * @file Loss.cpp
      25             :  * @author J. Rydzewski (jr@fizyka.umk.pl)
      26             :  */
      27             : 
      28             : #include "Loss.h"
      29             : 
      30             : namespace PLMD {
      31             : namespace maze {
      32             : 
      33             : //+PLUMEDOC MAZE_LOSS MAZE_LOSS
      34             : /*
      35             : 
      36             : Define a coarse-grained loss function describing interactions in a
      37             : ligand-protein complex, which is minimized during the simulation to
      38             : obtain ligand unbinding pathways.
      39             : 
      40             : The loss function is the following:
      41             : \f[
      42             : \mathcal{L}=
      43             : \sum_{i=1}^{N_p}
      44             : r_i^{-\alpha}\text{e}^{-\beta r_i^{-\gamma}},
      45             : \f]
      46             : where \f$N_p\f$ is the number of ligand-protein atom pairs, \f$r\f$
      47             : is a re-scaled distance between the \f$i\f$th pair, and \f$\alpha,
      48             : \beta, \gamma\f$ are the positive parameters defined in that order by
      49             : the PARAMS keyword.
      50             : 
      51             : \par Examples
      52             : 
      53             : The loss function can be defined in the following way:
      54             : \plumedfile
      55             : l: MAZE_LOSS PARAMS=1,1,1
      56             : \endplumedfile
      57             : 
      58             : */
      59             : //+ENDPLUMEDOC
      60             : 
      61             : // Registers the LOSS action.
      62       13801 : PLUMED_REGISTER_ACTION(Loss, "MAZE_LOSS")
      63             : 
      64          12 : void Loss::registerKeywords(Keywords& keys) {
      65          12 :   Colvar::registerKeywords(keys);
      66             : 
      67          24 :   keys.add(
      68             :     "compulsory",
      69             :     "PARAMS",
      70             :     "Parameters for the loss function."
      71             :   );
      72          12 : }
      73             : 
      74           8 : Loss::Loss(const ActionOptions& ao)
      75           8 :   : PLUMED_COLVAR_INIT(ao) {
      76          16 :   if (keywords.exists("PARAMS")) {
      77          16 :     parseVector("PARAMS", params_);
      78             : 
      79           8 :     plumed_massert(
      80             :       params_.size() == 3,
      81             :       "maze> PARAMS should be of size 3: alpha, beta, gamma\n"
      82             :     );
      83             : 
      84           8 :     plumed_massert(
      85             :       params_[0] > 0 && params_[1] > 0 && params_[2] > 0,
      86             :       "maze> Each parameter should be positive\n"
      87             :     );
      88             : 
      89           8 :     log.printf("maze> \t Loss parsed with parameters: ");
      90          32 :     for (size_t i = 0; i < params_.size(); ++i) {
      91          24 :       log.printf("%f ", params_[i]);
      92             :     }
      93           8 :     log.printf("\n");
      94             :   }
      95             : 
      96           8 :   checkRead();
      97           8 : }
      98             : 
      99    16239210 : double Loss::pairing(double distance) {
     100    16239210 :   double alpha = params_[0];
     101    16239210 :   double beta = params_[1];
     102    16239210 :   double gamma = params_[2];
     103             : 
     104    16239210 :   if (atoms.getUnits().getLengthString() == "nm") {
     105    16120080 :     distance *= 10.0;
     106             :   }
     107             : 
     108    16239210 :   return pow(distance, -alpha) * exp(-beta * pow(distance, gamma));
     109             : }
     110             : 
     111             : } // namespace maze
     112             : } // namespace PLMD