[gmx-users] bond deviation

sadhna sadhana at che.iitb.ac.in
Thu Jan 10 15:31:09 CET 2002

    I am trying to simulate protein in water for 1ns. I want to
equilibrate solvent before simulation because the protein is not
maintaining the desired structure due to large solvent forces.
I tried doing it by giving following in mdp file for em in water:
freezegrps           = protein SOL
freezedim            = Y Y Y N N N
but after starting mdrun for 1ns i am geeting fatal error;Bond deviates
more than half its own length

please tell me workaround for this problem


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