set xrange [0:2*pi] V1=-0.1 V2=0.95 V3=0.55 G1=0 G2=0 G3=0 amber_original(x)= V1 * ( 1 + cos(1*x + G1)) + V2 * (1 + cos(2*x + G2)) + V3 * (1 + cos(3*x + G3)) plot amber_original(x) w lp V1=0.1 G1=pi amber_shifted(x) = V1 * ( 1 + cos(1*x + G1)) + V2 * (1 + cos(2*x + G2)) + V3 * (1 + cos(3*x + G3)) replot amber_shifted(x) w lp #the RB-potential in gromacs is defined for the dihedral angle psi, # which relates to the usually used torsional angle phi by psi=phi-180° # To account for this, the coefficients Cn are multiplied by Cn*(-1)**n: C0=-1**0 *2.30120 C1=-1**1 *6.90360 C2=-1**2 *7.94960 C3=-1**3 *-9.20480 gromacs_original(x)= C0 + C1*cos(x) + C2 * (cos(x)**2) + C3 * (cos(x)**3) replot gromacs_original(x)/4.184 c0=1*2.71960 c1=-1*7.32200 c2=1*7.94960 c3=-1*-9.20480 gromacs_shifted(x)= c0 + c1*cos(x) + c2 * (cos(x)**2) + c3 * (cos(x)**3) replot gromacs_shifted(x)/4.184 lw 3 set term post eps color enhanced "Arial" 20 set out "dihedral_profiles.eps" rep