# #################################################################
# brownmove definition file for
# a polymer of 3 uncharged beads connected by off-center springs
# ("bead-train polymer")
# 
# This file is for demonstration only of how such a polymer would
# be defined for a brownmove simulation.
# 
# Tihamer Geyer, 2011
# #################################################################

# some constants:
# MASS > 0.0 allows to switch to LD propagation if desired
constant    MASS    0.0
# spring constant
constant    SPRING  1000.0
# rotational diff-coeff (note: ratio of D_trans vs D_rot defines the bead size)
constant    D_ROT   0.75

# length and offset of the off-center springs: the center-to-center
# distance of the beads should be 2.5 nm.
# Thus we have the constraint:  2*B_OFF + B_L = 2.5
# Example 1: short spring attached to the bead surface
constant    B_OFF   1.0
constant    B_L     0.5
# Example 2: springs hooked up at the bead centers => a "normal" polymer
# constant  B_OFF   0.0
# constant  B_L     2.5
# Example 3 (left as an exercise): anything inbetween
# :


Protein polyTrain
    position 0.0 0.0 0.0  0.0 0.0 1.0 0.0

    Bonds PolyBonds
        # label  length  spring_constant
        B01     $B_L    $SPRING
        B12     $B_L    $SPRING
    End

    
    Gestalt Bead0
        position -2.5 0.0 0.0  0.0 1.0 0.0 0.0
        # D0 D0_trans D0_rot mass radius
        D0  1.0  $D_ROT $MASS 1.0

        BondShape Hooks0
            $B_OFF 0.0 0.0  B01
        End

        VdwShape Inner0
            0.0 0.0 0.0 1.0     0
        End
    End Gestalt


    Gestalt Bead1
        position 0.0 0.0 0.0  0.0 1.0 0.0 0.0
        D0  1.0  $D_ROT $MASS 1.0

        BondShape Hooks0
            -$B_OFF 0.0 0.0     B01
            $B_OFF  0.0 0.0     B12
        End

        VdwShape Inner0
            0.0 0.0 0.0 1.0     0
        End
    End Gestalt

    
    Gestalt Bead2
        position 2.5 0.0 0.0  0.0 1.0 0.0 0.0
        D0  1.0  $D_ROT $MASS 1.0

        BondShape Hooks0
            -$B_OFF 0.0 0.0     B12
        End

        VdwShape Inner0
            0.0 0.0 0.0 1.0     0
        End
    End Gestalt
End