#BIOSYM dsl 3
set PROJECT acenm
begin

forcefield nonbond vdw summation_method = group_based


#illustration to show the differences between atomMovability
#exclusion and energy calculation exclusion
#If an atom is excluded using the atomMovability command,
#all energies (bond, angle, nonbond) involving that atom
#will be excluded

#case 1: all atoms movable
energy print energies = 1
database handle ener_h Energy.
$ener_h select "Internal" Values.Name e1; $ener_h get int1 Values.Value $e1
$ener_h select "Bond" Values.Name e1; $ener_h get b1 Values.Value $e1
$ener_h select "Angle" Values.Name e1; $ener_h get a1 Values.Value $e1
$ener_h select "Nonbond" Values.Name e1; $ener_h get nb1 Values.Value $e1

#case 2: exclude the movability of 1 atom
atomMovability set excluded ex1 "ACENM:ACE_1:HA1"
#note that both the nonbond and internal energies are different from case 1
energy print energies = 1
database handle ener_h Energy.
$ener_h select "Internal" Values.Name e1; $ener_h get int2 Values.Value $e1
$ener_h select "Bond" Values.Name e1; $ener_h get b2 Values.Value $e1
$ener_h select "Angle" Values.Name e1; $ener_h get a2 Values.Value $e1
$ener_h select "Nonbond" Values.Name e1; $ener_h get nb2 Values.Value $e1
atomMovability unset ex1

#case 3: exclude the internal energy calculation of 1 atom
System_SetExcludeInternalEnergy "ACENM:ACE_1:HA1"
#note that all the energies are the same as case 2
energy print energies = 1
database handle ener_h Energy.
$ener_h select "Internal" Values.Name e1; $ener_h get int3 Values.Value $e1
$ener_h select "Bond" Values.Name e1; $ener_h get b3 Values.Value $e1
$ener_h select "Angle" Values.Name e1; $ener_h get a3 Values.Value $e1
$ener_h select "Nonbond" Values.Name e1; $ener_h get nb3 Values.Value $e1
System_SetExcludeInternalEnergy "ACENM:ACE_1:HA1" Include

#case 4: exclude the internal energy calculation of 2 atoms
System_SetExcludeInternalEnergy "ACENM:ACE_1:(CA,HA1)"
#note that the nonbond energy is unchanged but the internal energy is changed
#note that the bond energy is now the same as that in case 1
energy print energies = 1
database handle ener_h Energy.
$ener_h select "Internal" Values.Name e1; $ener_h get int4 Values.Value $e1
$ener_h select "Bond" Values.Name e1; $ener_h get b4 Values.Value $e1
$ener_h select "Angle" Values.Name e1; $ener_h get a4 Values.Value $e1
$ener_h select "Nonbond" Values.Name e1; $ener_h get nb4 Values.Value $e1
System_SetExcludeInternalEnergy "ACENM:ACE_1:(CA,HA1)" Include

echo \n\nEnergies\nnonbond, internal, bond, angle\n\n\n\
case 1:\n \
all atoms movable\n \
[vector nb1] [vector int1], [vector b1], [vector a1]\n\n\
case 2:\n \
exclude the movability of a carbon atom\n \
[vector nb2] [vector int2], [vector b2], [vector a2]\n\n\
case 3:\n \
exclude the internal energy calculation of the same as in case 2\n \
[vector nb3] [vector int3], [vector b3], [vector a3]\n \
note that all the energies are the same as case 1\n\n\
case 4:\n \
exclude the internal energy calculation of carbon and hydrogen atoms(C-H bond)\n \
[vector nb4] [vector int4], [vector b4], [vector a4]\n \
note that:\n \
the nonbond energy is the same as case 1\n \
the bond energy is the same as case 2\n \
the angle energy is the same as case 1