I am trying to separate two methyl-N,N'-diacetylchitobiose sugars using steered molecular dynamics in AMBER. I have tested out:
&rst iat=-1,-1, r2=2.5, rk2=10.0, r2a=12.5, iresid=0, fxyz=1,1,1, outxyz=1, igr1=2,5,6,8,9,11,14,16,18,20,22,24,26,27,28,32,33,35,36,38,41,43,45,47,49,51,53,54,55,59,60, igr2=65,68,69,71,72,74,77,79,81,83,85,87,89,90,91,95,96,98,99,101,104,106,108,110,112,114,116,117,118,122,123 /
Which should apparently separate the two sugars relative to their heavy atoms from a distance (between each other) of 2.5 A to 12.5 A along the x,y and z axes and using a force constant of 10 (I think kcal/mol). The solvent I am using is water.
I ran this separation for 100 ns and the two sugars refused to separate. I am not sure if my force constant is too small, or if something else is wrong with my reference file. I have googled it and spoken to m supervisor about it, and unfortunately I have not succeeded in finding a solution.
Any help would be appreciated.