I am trying to separate two methyl-N,N'-diacetylchitobiose sugars using steered molecular dynamics in AMBER. I have tested out:


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.

  • 1
    $\begingroup$ Are you sure you have specified the correct groups/residue IDs/atom numbers? If yes, then have you tried increasing the force constant to a very high value, to see whether or not the molecules separate? $\endgroup$
    – Bdrs
    Jun 6 '18 at 8:53
  • 1
    $\begingroup$ The force constant was too low. I managed to fix it now. $\endgroup$
    – LLCJ27
    Jun 6 '18 at 10:32

I have realized the problem. The force constant was too low. Increasing it to 25.0 from 10.0 sorted things out.


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