Hi all,
I want to build elastic network model using gromacs. I consider
only c-alpha atoms and only bond stretching term contributes to towards
potential energy. Bonds are connected between atoms present with in
certain cut-off distance(modified topology accordingly). When I run md the
atoms are not present at the equillibrium distance but moving very far
distances , in different directions. I do not want to use constraints. How
can i avoid this?
2) Has anyone built elastic network model in gromacs?
Please suggest me a way,
Thank you in advance,
Mohan.
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