AMBER Archive (2002)

Subject: atoms coming too close during MD (with SHAKE on)

From: Pratul Agarwal (pratulka_at_rocketmail.com)
Date: Mon Sep 02 2002 - 20:01:18 CDT

I noticed that during my MD runs there are several Hydrogen atoms which
are making very close contact with non-bonded heavy atoms and other
Hydrogens (as close as 1.4 Angstroms) . This causes the energy to
fluctuate widely, varying upto 200 kcal/mol per step (most of which is
coming from the Lennard-Jones replusion term).

The system is a TIP3P solvated protein-DNA complex. I have
equilibriated it will (several minimization steps + 400 ps MD). I do
have SHAKE on for the bonds involving Hydrogens, therefore I am using a
time step of 2 fs (ntc=2, ntf=2, dt=0.002). There are no
restraints/constraints on any of the "colliding" atoms.

Has anybody ever seen anything like this before? Any idea where the
problem could be?
If you need more information let me know.

I am currently redoing the MD runs with no SHAKE (dt =0.001 obviously).
But I am concerned because I am using TIP3P model for my solvent, as
far as my understanding goes SHAKE is recommended to be used for a
rigid 3-point model for water. Is there a way to turn on SHAKE only for solvent?

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