remarks nmr/random.inp   
remarks  The ultimate simulated annealing protocol for NMR structure 
remarks  determination!
remarks  The starting structure for this protocol can be completely 
remarks  arbitrary, such as random numbers.  Note: the resulting
remarks  structures need to be further processed by the dgsa.inp protocol. 
remarks  Reference: Nilges, Clore, and Gronenborn 1988a. 
remarks Author: Michael Nilges

{====>}
evaluate ($init_t = 1000 )      {* Initial simulated annealing temperature.*}


parameter                                        {*Read the parameter file.*}
{====>} 
   @TOPPAR:parallhdg.pro
end

{====>}
structure @g_protein.psf end                     {*Read the structure file.*}
  
noe 
{====>}                                                        
   nres=3000             {*Estimate greater than the actual number of NOEs.*}
   class all 
{====>} 
   @g_protein_noe.tbl                           {*Read NOE distance ranges.*}
end

{====>} 
@g_protein_dihe.tbl                       {*Read dihedral angle restraints.*}


noe                             {*Parameters for NOE effective energy term.*}
  ceiling=1000                     
  averaging  * cent
  potential  * soft
  scale      * 1                          
  sqoffset   * 0.0  
  sqconstant * 1.0
  sqexponent * 2
  soexponent * 1
  asymptote  * 2.0                      {* Initial value - modified later. *}
  rswitch    * 1.0
end
 
set message=off end

{====>} evaluate ($end_count=10)                  {* Number of structures. *} 

evaluate ($count = 0)
while ($count < $end_count ) loop main 
    evaluate ($count=$count+1)
    
                                         {* Generate a starting structure. *}
    vector do (x = (random()-0.5)*20) (all) 
    vector do (y = (random()-0.5)*20) (all)
    vector do (z = (random()-0.5)*20) (all)

    vector do (fbeta=10) (all)      {*Friction coefficient for MD heatbath.*}
    vector do (mass=100) (all)              {*Uniform heavy masses to speed*}
                                            {*molecular dynamics.          *}

    parameter nbonds 
         atom cutnb 100 tolerance 45 repel=1.2 
         rexp=2 irexp=2 rcon=1.0 nbxmod 4
    end end
        
    flags exclude * include bonds angle impr vdw noe cdih  harm end
    
    evaluate ($knoe = 0.5)   

    evaluate ($kbon = 0.00005  )                 {* Bonds.                 *}
    evaluate ($kang = 0.00005  )                 {* Angles.                *}
    evaluate ($kimp = 0.0  )                     {* Impropers.             *}
    evaluate ($kvdw = 0.1)                       {* Vdw.                   *} 
    constraints 
        interaction (not name ca) (all) 
        weights bond $kbon angl $kang impr $kimp vdw 0 elec 0 end 
        interaction (name ca) (name ca) 
        weights bond $kbon angl $kang impr $kimp vdw $kvdw end 
    end
    
      
    {* ======================================== High temperature dynamics. *}
      
    vector do (vx = maxwell($init_t)) (all)
    vector do (vy = maxwell($init_t)) (all)
    vector do (vz = maxwell($init_t)) (all)

    evaluate ($timestep = 0.04)
    evaluate ($nstep = 100)

    while ($kbon < 0.01) loop stage1
      
            evaluate ($kbon = min(0.25, $kbon * 1.25))
            evaluate ($kang = $kbon)
            evaluate ($kimp = 0)
	   
            noe scale * $knoe end
            restraints dihed scale 0. end 
            constraints 
                interaction (not name ca) (all) 
                weights bond $kbon angl $kang impr $kimp vdw 0 elec 0 end 
                interaction (name ca) (name ca) 
                weights bond $kbon angl $kang impr $kimp vdw $kvdw end 
            end
	    	    
            dynamics  verlet
                  nstep=$nstep   timestep=$timestep   iasvel=current   
                  tcoupling=true tbath=$init_t  nprint=50  iprfrq=0 
            end	    
	    
    end loop stage1

    restraints dihed scale 0. end
    noe scale * 5 end
    parameter                {* Parameters for the repulsive energy term.  *}
      nbonds
        repel=0.9            {* Initial value for repel - modified later.  *}
        nbxmod=-3            {* Initial value for nbxmod - modified later. *}
        wmin=0.01 
        cutnb=4.5 ctonnb=2.99 ctofnb=3. 
        tolerance=0.5 
      end
    end
    constraints 
                interaction (all) (all) 
                weights bond 0.02 angl 0.02 impr 0 vdw 0.002 elec 0 end 
    end
    dynamics  verlet
                nstep=500   timestep=0.003   iasvel=maxwell   
                firstt=1500
                tcoupling=true 
                tbath=1500  nprint=50  iprfrq=0 
    end
    constraints
                interaction (all) (all) 
                weights bond 0.05 angl 0.05 impr 0 vdw 0.005 elec 0 end 
    end
    dynamics  verlet
                  nstep=500   timestep=0.003   iasvel=current  tcoupling=true 
                  tbath=1500  nprint=50  iprfrq=0 
    end
    constraints 
                interaction (all) (all) 
                weights bond 0.1 angl 0.1 impr 0 vdw 0.01 elec 0 end 
    end
    dynamics  verlet
                  nstep=500   timestep=0.003   iasvel=current  tcoupling=true 
                  tbath=1500  nprint=50  iprfrq=0 
    end

   {* =================================== Write out the final structure(s).*}
   remarks =============================================================== 
   remarks            overall,bonds,angles,improper,vdw,noe,cdih
   remarks energies: $ener, $bond, $angl, $impr, $vdw, $noe, $cdih 
    

{===>}                         {*Name(s) of the family of final structures.*}
   evaluate ($filename="random_"+encode($count)+".pdb")
      
   write coordinates output =$filename end

end loop main

stop