ADD_STR_COM

NAME
ADD_STR_COM - Add a bond potential between the Centers of Mass (COMs) of two selected group of atoms.

SYNOPSIS
ADD_STR_COM

ligand ilig1 ilig2

target itar1 itar2

force kcom r0com [r1com]
END

DESCRIPTION
This command can be used to impose an additional bond restraint potential (with force constant kcom [ in kcal mol$^{-1}$ ] and equilibrium distance r0com) ( in Å) between the COM of a ``ligand'', defined by the atoms subset ilig1-ilig2, and the COM of a ``target'', defined by the the atoms subset itar1-itar2. If the optional parameter r1com is also specified then a steered molecular dynamics is implied (see also STEER command).

WARNINGS
Experimental - Unsupported

EXAMPLES

• Example 1
  

   
  &POTENTIAL 
    ...
    ADD_STR_COM
      ligand  1 10 
      target  11 1500
      force   10.0 5.0 
    END
    ...
  &END
  

• Example 2.
  

   
  &POTENTIAL 
    ...
    ADD_STR_COM
      ligand  1 10 
      target  11 1500
      force   10.0 5.0  10.0 
    END
   ..
  &END
  ....
  ...
  &RUN
     ...
     STEER 10000.  50000. 
     ...
  &END
  

In the first example a COM-COM restraint at r= 5.0 Å  is imposed between the ligand (first 10 atoms as labeled in the output PDB) and a 1489 atoms target with atomic labels going from 11 to 1500. In the second example the restraint potential is steered at constant speed from 5 to 10 Å  in the time span 10 - 50 ps.