Plumed interface

Iphigenie supports the plugin metadynamics library PLUMED, if it is compiled accordingly. It can be activated in the freeEnergy section by

<freeEnergy>
  <plumed>
    <!--read plumed input from file                                              -->
    <input>plumed.inp</input>
    <!--write plumed output to file                                              -->
    <output>plumed.out</output>
    <!--write plumed forces for selected atoms-->
    <forces></forces>
  </plumed>
</freeEnergy>

If discreteTempering is turned on as well, i.e. one has multiple rungs and one or more replicas, one can use PLUMED for Hamilton replica exchange by additionally using

 <HamiltonReplicaExchange>
      <plumed>true</plumed>
 </HamiltonReplicaExchange>

Then you have to provide a PLUMED input file for each rung, e.g. plumed.inp000, plumed.inp001, ..., i.e. the input name specified above appended by the three digit rung number. For example, for a umbrella sampling Hamilton replica exchange rung one could use a PLUMED input like

rung: CONSTANT VALUE=0
mi4:  COM ATOMS=1-12
pam:  COM ATOMS=13-24
d:    DISTANCE ATOMS=mi4,pam
rstr: RESTRAINT ARG=d KAPPA=1.0 AT=4.0
PRINT ARG=rung,rstr.bias,d  STRIDE=100 FMT=%g

for rung 0 to compute the potential of mean force between the molecules MI4 and PAM. For the other rungs one uses correspondingly their rung index and higher AT values.

Note that all replica exchange functionalities (eg. RANDOM_EXCHANGES) within PLUMED are not supported --- all exchanges are handled within iffi. Using metadynamics with bias exchange would probably be possible but would require a special setup.