Distance restraints

From: Paula Mihaljevic-Juric (paula.mihaljevic-juric_at_polytechnique.edu)
Date: Fri Oct 04 2019 - 02:21:47 CDT

Hi

Can I apply distance restraints in a same way secondary structure restraints are applied in MDFF or do I have to use colvars variables to apply them?

I wanted to define in a separate files with fc and reference distance for each atom and use sth like

if {$EXTRAB != 0} {
  extraBonds yes
  foreach fil $EXTRAB {
    extraBondsFile $fil
  }
}

To read them. Would this be sufficient?

If I am not able to use this, how can I define distance restraints using colvars, I would appreciate some explaining me the procedure including what am I supposed to put in the pdf file.

Thank you
Paula

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