[gmx-users] elastic network model - atoms movement

mohan maruthi sena maruthi.sena at gmail.com
Tue Sep 25 15:51:28 CEST 2012

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,

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