From: Marcela P.Aliste (marcela.aliste_at_biology.gatech.edu)
Date: Thu Feb 24 2005 - 16:14:26 CST
I used NAMD before:
I change to AMBER topology to calculate protein-RNA interaction.
The problem is with the water model TIP3, that AMBER generate the third
bond, but there are not
definition for angle. I tried 2 fs time step using SHAKE algorithm, and
the simulation crush after 1 step.
I changed to 1 fs without using SHAKE. it is running. but it will take
twice the time.
How can I fix this problem using AMBER & shake.
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