The other covalent bonds chnaging during constarined MD

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Annesha Debroy

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Oct 14, 2021, 3:14:37 AMOct 14
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Dear group,

I am performing constrained dynamics for a system containing two organic molecules and water. I set the distance between inter molecular atoms (i.e. C and C) for a range of values. Now,  when I set the distance to arbitrary value, my C and C distance does change to tthat value but other bonds that C atoms are attached with also change. This leads the system to be unstable at larger values of C and C separation as other covalent bond now are too small and the structure is very unstable. The tutorial for constrained MD, of deca alanine, also the other bond distances are changing other than the one we want. Please help me.
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