Hydrogens collapsing

From: Vishal Kopardé (vnk_sim_at_yahoo.co.uk)
Date: Wed Nov 01 2006 - 21:20:50 CST

Hi all,
        While trying to equilibrate my protein (no solvent yet), I find that
I get RATTLE error all the time and the atom involved in the error is
always N. Upon observing the dcd file in VMD, it seems that the
Hydrogens bonded to the N atom ( which is different if timestep/
temperature is changed) collapse into one another. The collapsed H
atoms must be exerting unnatural forces on N atom leading to RATTLE
        Can anyone tell me how H-H interactions are managed in NAMD. Is
there a constraint for H-N-H angle in NH2 group, just like in H2O? I
think I am missing something here... dont know what. Your suggestions
are welcome.
Thank you,

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