ADD_STR_BONDS

NAME
ADD_STR_BONDS - Add a stretching potential between two target atoms.

SYNOPSIS
ADD_STR_BONDS    iat1    iat2    k    $r_0$    [ $r_{\tau}$]

DESCRIPTION
This command can be used to impose an additional stretching constraint between atom iat1 and iat2 of the solute. The numeric order of the solute atom indices iat1, iat2 is that specified in the topology file (see 10.3). The added stretching potential has force constant k (in Kcal/mol/Å$^{2}$) and equilibrium distance $r_0$ (in Å). If $r_\tau$ is also specified, then the added stretching potential is time dependent and $r_{\tau}$ is the equilibrium distance after the steering time $\tau$ (see STEER(&RUN)) command for the definition of the steering time in a SMD simulation)

[]WARNINGS
If the chosen $r_0$ is very different from the actual value of the distance $\vert{\bf r}_{\rm iat1} - {\bf r}_{\rm iat2} \vert$ at time 0, a very large force is experienced by the atoms in involved in the added stretching and the simulation may catastrophically diverge after few steps. []EXAMPLES

• Example 1.
  

   
  ADD_STR_BONDS  1 104  400.  31.5
  

• Example 2.
  

   
  &PARAMETERS
     READ_TPGPRM_BIN  ala10_A.prmtpg
  &END
  
  ...
  &POTENTIAL 
    ...
    ADD_STR_BONDS  1 104  400.  31.5  15.5
   ..
  &END
  ....
  ...
  &RUN
     CONTROL 2
     ...
     REJECT 0.0 
     STEER 10000.  50000.  
     TIME 50009.0
     ...
  &END 
  ..
  &INOUT
     RESTART 
        rmr ../RESTART/ala10 0 
  &END
  

In the first example a stretching constraint is imposed between atom 1 and atom 104 of the solute. In the second example a time-dependent driving potential is applied to the same atoms of the solute. The equilibrium distance of such harmonic driving potential move at constant velocity in $\tau=40$ ps (starting at t=10 ps ) between $r_0=31.5$ and $r_\tau=15.5$. Since the directive rmr (or read_multiple_restart ) is issued in the RESTART(&INOUT) command, the example is assumed to run in parallel. Each process reads a different restart file named ala10$iproc$.rst in the ../RESTART directory. Note that the path of the restart files is specified with respect to the actual value of the pwd command when the parallel version is executed (i.e. in the $PARxxxx$ directories).