Hi all, There are atoms (a1 and a2) in my small molecule coordinate file that have the same z component: a1: atom#22 (x1,y1,60.231) a2: atom#45 (x2,y2,60.231)If I use these lines only
Therefore the vector a1-a2 makes theta=90o with the z-axis. in my previous MD runs the a1-a2 were flexible (theta was observed in the range of 30-120 degrees). To restrain a1-a2 at this orientation throughout my MD calculations I included these lines to my starting topology: ; Restrain the molecules wrt z-axis... [ angle_restraints_z ] ; #1 #2 type theta0(degrees) k_c(kJ mpl^(-1)) multiplicity 22 45 1 90 1000 1 Would someone comment on: - Is this is all I need to do to restrain a1-12 wrt z-axis? - Are the above parameters (theta/K/multiplicity) reasonable/correct? - with this I should expect a1 and a2 stay in xy-plane (with their z component equal at each frame) during minimization, equilibration and production? Thanks. -- Cheers, Terry
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