AMBER Archive (2005)

Subject: AMBER: shake

From: Gustavo Pierdominici Sottile (gsottile_at_unq.edu.ar)
Date: Fri Aug 19 2005 - 11:37:46 CDT

Dear list,
         I want to run a dynamic with explicit solvent (tip3p model). In the
DNA tutorial, it is mentioned that when using such a water model it is
essential that the hydrogen atom motion of the water also be fixed since
failure to do this can lead to very large inaccuracies in the calculation of
the densities,etc. I can not use SHAKE because the dynamics of an hydrogen
atom is what I want to see. Is the any way to constrain only the hydrogen
atoms of water molecules?. If this is not possible, is it possible to leave
SHAKE off, using tip3p?
Thanking in advance
Gustavo

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